[
https://issues.apache.org/jira/browse/SPARK-27076?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
srinivas rao gajjala updated SPARK-27076:
-----------------------------------------
Summary: Getting the timeout error while reading parquet/csv files from s3
(was: Getting the timeout error while reading parquet files from s3)
> Getting the timeout error while reading parquet/csv files from s3
> -----------------------------------------------------------------
>
> Key: SPARK-27076
> URL: https://issues.apache.org/jira/browse/SPARK-27076
> Project: Spark
> Issue Type: Bug
> Components: Spark Core
> Affects Versions: 2.2.0
> Reporter: srinivas rao gajjala
> Priority: Major
>
> Hi,
> I'm trying to read parquet files from s3 using Amazon EMR clusters with the
> lable(emr-5.9.0) and below is the error I'm facing.
> {code:java}
> org.apache.spark.SparkException: Job aborted. at
> org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:215)
> at
> org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:173)
> at
> org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:173)
> at
> org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65)
> at
> org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:173)
> at
> org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:145)
> at
> org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58)
> at
> org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56)
> at
> org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74)
> at
> org.apache.spark.sql.execution.SparkPlan$$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$lzycompute(QueryExecution.scala:92)
> at
> org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:92)
> at
> org.apache.spark.sql.execution.datasources.DataSource.writeInFileFormat(DataSource.scala:438)
> at
> org.apache.spark.sql.execution.datasources.DataSource.write(DataSource.scala:474)
> at
> org.apache.spark.sql.execution.datasources.SaveIntoDataSourceCommand.run(SaveIntoDataSourceCommand.scala:48)
> at
> org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$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$$anonfun$executeQuery$1.apply(SparkPlan.scala:138)
> at
> org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
> at
> org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:135) at
> org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:116) at
> org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:92)
> at
> org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:92)
> at org.apache.spark.sql.DataFrameWriter.runCommand(DataFrameWriter.scala:610)
> at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:233) at
> org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:217) at
> org.apache.spark.sql.DataFrameWriter.csv(DataFrameWriter.scala:598) at
> DataFrameFromTo.dataFrameToFile(DataFrameFromTo.scala:120) at
> Migration.migrate(Migration.scala:211) at
> DataMigrationFramework$$anonfun$main$3$$anonfun$apply$mcV$sp$1.apply$mcVI$sp(DataMigrationFramework.scala:353)
> at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:160) at
> DataMigrationFramework$$anonfun$main$3.apply$mcV$sp(DataMigrationFramework.scala:351)
> at scala.util.control.Breaks.breakable(Breaks.scala:38) at
> DataMigrationFramework$.main(DataMigrationFramework.scala:350) at
> DataMigrationFramework.main(DataMigrationFramework.scala) at
> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498) at
> org.apache.spark.deploy.yarn.ApplicationMaster$$anon$2.run(ApplicationMaster.scala:635)
> Caused by: org.apache.spark.SparkException: Job aborted due to stage
> failure: Task 1120 in stage 5.0 failed 16 times, most recent failure: Lost
> task 1120.15 in stage 5.0 (TID 8886, ip-10-120-60-82.ec2.internal, executor
> 4): com.amazonaws.SdkClientException: Unable to execute HTTP request: Timeout
> waiting for connection from pool at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleRetryableException(AmazonHttpClient.java:1068)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1034)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:741)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:715)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:697)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:665)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:647)
> at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:511) at
> com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4227) at
> com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4174) at
> com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1253)
> at
> com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1228)
> at
> org.apache.hadoop.fs.s3a.S3AFileSystem.getFileStatus(S3AFileSystem.java:903)
> at
> org.apache.hadoop.fs.s3a.S3AFileSystem.getFileStatus(S3AFileSystem.java:77)
> at
> org.apache.parquet.hadoop.util.HadoopInputFile.fromPath(HadoopInputFile.java:39)
> at
> org.apache.parquet.hadoop.ParquetFileReader.readFooter(ParquetFileReader.java:401)
> at
> org.apache.spark.sql.execution.datasources.parquet.SpecificParquetRecordReaderBase.initialize(SpecificParquetRecordReaderBase.java:106)
> at
> org.apache.spark.sql.execution.datasources.parquet.VectorizedParquetRecordReader.initialize(VectorizedParquetRecordReader.java:109)
> at
> org.apache.spark.sql.execution.datasources.parquet.ParquetFileFormat$$anonfun$buildReaderWithPartitionValues$1.apply(ParquetFileFormat.scala:363)
> at
> org.apache.spark.sql.execution.datasources.parquet.ParquetFileFormat$$anonfun$buildReaderWithPartitionValues$1.apply(ParquetFileFormat.scala:337)
> at
> org.apache.spark.sql.execution.datasources.FileScanRDD$$anon$1.org$apache$spark$sql$execution$datasources$FileScanRDD$$anon$$readCurrentFile(FileScanRDD.scala:124)
> at
> org.apache.spark.sql.execution.datasources.FileScanRDD$$anon$1.nextIterator(FileScanRDD.scala:174)
> at
> org.apache.spark.sql.execution.datasources.FileScanRDD$$anon$1.hasNext(FileScanRDD.scala:105)
> at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.scan_nextBatch$(Unknown
> Source) at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithKeys$(Unknown
> Source) at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
> Source) at
> org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
> at
> org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
> at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) at
> org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:125)
> at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96) at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53) at
> org.apache.spark.scheduler.Task.run(Task.scala:108) at
> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335) 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: org.apache.http.conn.ConnectionPoolTimeoutException: Timeout
> waiting for connection from pool at
> org.apache.http.impl.conn.PoolingHttpClientConnectionManager.leaseConnection(PoolingHttpClientConnectionManager.java:292)
> at
> org.apache.http.impl.conn.PoolingHttpClientConnectionManager$1.get(PoolingHttpClientConnectionManager.java:269)
> at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source) at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498) at
> com.amazonaws.http.conn.ClientConnectionRequestFactory$Handler.invoke(ClientConnectionRequestFactory.java:70)
> at com.amazonaws.http.conn.$Proxy11.get(Unknown Source) at
> org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:191)
> at
> org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:185) at
> org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:185)
> at
> org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:83)
> at
> org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:56)
> at
> com.amazonaws.http.apache.client.impl.SdkHttpClient.execute(SdkHttpClient.java:72)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1189)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1029)
> ... 35 more Driver stacktrace: at
> org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1690)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1678)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1677)
> at
> scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
> at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48) at
> org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1677)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
> at scala.Option.foreach(Option.scala:257) at
> org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:855)
> at
> org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1905)
> at
> org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1860)
> at
> org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1849)
> at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48) at
> org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:671) at
> org.apache.spark.SparkContext.runJob(SparkContext.scala:2022) at
> org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:188)
> ... 47 more Caused by: com.amazonaws.SdkClientException: Unable to execute
> HTTP request: Timeout waiting for connection from pool at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleRetryableException(AmazonHttpClient.java:1068)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1034)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:741)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:715)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:697)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:665)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:647)
> at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:511) at
> com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4227) at
> com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4174) at
> com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1253)
> at
> com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1228)
> at
> org.apache.hadoop.fs.s3a.S3AFileSystem.getFileStatus(S3AFileSystem.java:903)
> at
> org.apache.hadoop.fs.s3a.S3AFileSystem.getFileStatus(S3AFileSystem.java:77)
> at
> org.apache.parquet.hadoop.util.HadoopInputFile.fromPath(HadoopInputFile.java:39)
> at
> org.apache.parquet.hadoop.ParquetFileReader.readFooter(ParquetFileReader.java:401)
> at
> org.apache.spark.sql.execution.datasources.parquet.SpecificParquetRecordReaderBase.initialize(SpecificParquetRecordReaderBase.java:106)
> at
> org.apache.spark.sql.execution.datasources.parquet.VectorizedParquetRecordReader.initialize(VectorizedParquetRecordReader.java:109)
> at
> org.apache.spark.sql.execution.datasources.parquet.ParquetFileFormat$$anonfun$buildReaderWithPartitionValues$1.apply(ParquetFileFormat.scala:363)
> at
> org.apache.spark.sql.execution.datasources.parquet.ParquetFileFormat$$anonfun$buildReaderWithPartitionValues$1.apply(ParquetFileFormat.scala:337)
> at
> org.apache.spark.sql.execution.datasources.FileScanRDD$$anon$1.org$apache$spark$sql$execution$datasources$FileScanRDD$$anon$$readCurrentFile(FileScanRDD.scala:124)
> at
> org.apache.spark.sql.execution.datasources.FileScanRDD$$anon$1.nextIterator(FileScanRDD.scala:174)
> at
> org.apache.spark.sql.execution.datasources.FileScanRDD$$anon$1.hasNext(FileScanRDD.scala:105)
> at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.scan_nextBatch$(Unknown
> Source) at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithKeys$(Unknown
> Source) at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
> Source) at
> org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
> at
> org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
> at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408) at
> org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:125)
> at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96) at
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53) at
> org.apache.spark.scheduler.Task.run(Task.scala:108) at
> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335) 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:
> org.apache.http.conn.ConnectionPoolTimeoutException: Timeout waiting for
> connection from pool at
> org.apache.http.impl.conn.PoolingHttpClientConnectionManager.leaseConnection(PoolingHttpClientConnectionManager.java:292)
> at
> org.apache.http.impl.conn.PoolingHttpClientConnectionManager$1.get(PoolingHttpClientConnectionManager.java:269)
> at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source) at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498) at
> com.amazonaws.http.conn.ClientConnectionRequestFactory$Handler.invoke(ClientConnectionRequestFactory.java:70)
> at com.amazonaws.http.conn.$Proxy11.get(Unknown Source) at
> org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:191)
> at
> org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:185) at
> org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:185)
> at
> org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:83)
> at
> org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:56)
> at
> com.amazonaws.http.apache.client.impl.SdkHttpClient.execute(SdkHttpClient.java:72)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1189)
> at
> com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1029)
> ... 35 more at
> {code}
> I saw few issues of this sort for avro formats, please let me know if I'm
> missing something. Thanks
>
--
This message was sent by Atlassian JIRA
(v7.6.3#76005)
---------------------------------------------------------------------
To unsubscribe, e-mail: [email protected]
For additional commands, e-mail: [email protected]
