spark streaming job suddenly exits on FileNotFoundException - apache-spark

Question

I am running a Spark streaming application where each batches writes its final output to S3 in parquet format by using SqlContext.
I am able to get this application to run successfully in EMR.
However, after running for a couple of hours, the spark jobs suddenly halts on a FileNotFoundException.
I am not sure what to do next here.
Any pointers in how to debug/fix this issue would be useful.
I use Spark 2.2.1, EMR 5.1.1 and Java 8 for my application.
My streaming application code
public class StreamingApp {
JavaStreamingContext initDAG() {
JavaSparkContext sc = new JavaSparkContext(sparkConf);
// new context
JavaStreamingContext jssc = new JavaStreamingContext(sc, batchInterval);
SQLContext sqlContext = new SQLContext(sc);
...
// Converting to Dataset's Row type
JavaDStream<Row> rowStream = inputStream.map(new ObjectToRowMapperFunction());
// Writing to Disk
rowStream.foreachRDD(new RddToParquetFunction(sqlContext));
return jssc;
}
...
}
public class RddToParquetFunction implements VoidFunction<JavaRDD<Row>> {
private final StructType userStructType;
private final SQLContext sqlContext;
public RddToParquetFunction(SQLContext sqlContext) {
userStructType = ProtobufSparkStructMapper.schemaFor(UserMessage.class);
this.sqlContext = sqlContext;
}
#Override
public void call(JavaRDD<Row> rowRDD) throws Exception {
Dataset<Row> userDataFrame = sqlContext.createDataFrame(rowRDD, userStructType);
userDataFrame.write().mode(SaveMode.Append).parquet("s3://XXXXXXX/XXXXX/");
}
}
appropriate spark driver logs
18/02/15 22:47:57 ERROR ApplicationMaster: User class threw exception: org.apache.spark.SparkException: Job aborted.
org.apache.spark.SparkException: Job aborted.
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:213)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:166)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:166)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:166)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:145)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(comm ands.scala:58)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:138)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:135)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:116)
at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:92)
at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:92)
at org.apache.spark.sql.execution.datasources.DataSource.writeInFileFormat(DataSource.scala:435)
at org.apache.spark.sql.execution.datasources.DataSource.write(DataSource.scala:471)
at org.apache.spark.sql.execution.datasources.SaveIntoDataSourceCommand.run(SaveIntoDataSourceCommand.scala:50)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:138)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:135)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:116)
at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:92)
at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:92)
at org.apache.spark.sql.DataFrameWriter.runCommand(DataFrameWriter.scala:609)
at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:233)
at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:217)
at org.apache.spark.sql.DataFrameWriter.parquet(DataFrameWriter.scala:508)
at app.functions.RddToParquetFunction.call(RddToParquetFunction.java:37)
at app.functions.RddToParquetFunction.call(RddToParquetFunction.java:17)
at org.apache.spark.streaming.api.java.JavaDStreamLike$$anonfun$foreachRDD$1.apply(JavaDStreamLike.scala:272)
at org.apache.spark.streaming.api.java.JavaDStreamLike$$anonfun$foreachRDD$1.apply(JavaDStreamLike.scala:272)
at org.apache.spark.streaming.dstream.DStream$$anonfun$foreachRDD$1$$anonfun$apply$mcV$sp$3.apply(DStream.scala:628)
at org.apache.spark.streaming.dstream.DStream$$anonfun$foreachRDD$1$$anonfun$apply$mcV$sp$3.apply(DStream.scala:628)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ForEachDStream.scala:51)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1$$anonfun$apply$mcV$sp$1.apply(ForEachDStream.scala:51)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1$$anonfun$apply$mcV$sp$1.apply(ForEachDStream.scala:51)
at org.apache.spark.streaming.dstream.DStream.createRDDWithLocalProperties(DStream.scala:416)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1.apply$mcV$sp(ForEachDStream.scala:50)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1.apply(ForEachDStream.scala:50)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1.apply(ForEachDStream.scala:50)
at scala.util.Try$.apply(Try.scala:192)
at org.apache.spark.streaming.scheduler.Job.run(Job.scala:39)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler$$anonfun$run$1.apply$mcV$sp(JobScheduler.scala:257)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler$$anonfun$run$1.apply(JobScheduler.scala:257)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler$$anonfun$run$1.apply(JobScheduler.scala:257)
at scala.util.DynamicVariable.withValue(DynamicVariable.scala:58)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler.run(JobScheduler.scala:256)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.FileNotFoundException: File s3://XXXXXXX/XXXXX/output/_temporary/0/task_20180215224653_0267_m_000032 does not exist.
at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.listStatus(S3NativeFileSystem.java:996)
at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.listStatus(S3NativeFileSystem.java:937)
at com.amazon.ws.emr.hadoop.fs.EmrFileSystem.listStatus(EmrFileSystem.java:337)
at org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter.mergePaths(FileOutputCommitter.java:426)
at org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter.commitJobInternal(FileOutputCommitter.java:362)
at org.apache.hadoop.mapreduce.lib.output.FileOutputCommitter.commitJob(FileOutputCommitter.java:334)
at org.apache.parquet.hadoop.ParquetOutputCommitter.commitJob(ParquetOutputCommitter.java:47)
at org.apache.spark.internal.io.HadoopMapReduceCommitProtocol.commitJob(HadoopMapReduceCommitProtocol.scala:142)
at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:207)
... 57 more

Answer 1

Unless you pay the premium for Amazon's consistent EMR you can't reliably use S3 as a destination for your work.
ASF Hadoop+ Spark has fixed this on Hadoop 3.1+ with the S3A committers. Without that, and on amazon EMR, you need to write to HDFS and then use distcp to copy up the results if needed. If chaining together work, leave on HDFS.