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Posted to issues@spark.apache.org by "Sean Owen (JIRA)" <ji...@apache.org> on 2016/11/11 11:01:03 UTC
[jira] [Commented] (SPARK-18402) spark: SAXParseException while
writing from json to parquet on s3
[ https://issues.apache.org/jira/browse/SPARK-18402?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15656772#comment-15656772 ]
Sean Owen commented on SPARK-18402:
-----------------------------------
This is an error from Amazon / its SDK, not Spark.
> spark: SAXParseException while writing from json to parquet on s3
> -----------------------------------------------------------------
>
> Key: SPARK-18402
> URL: https://issues.apache.org/jira/browse/SPARK-18402
> Project: Spark
> Issue Type: Bug
> Components: Spark Core, Spark Submit
> Affects Versions: 1.6.2, 2.0.1
> Environment: spark 2.0.1 hadoop 2.7.1
> hadoop aws 2.7.1
> ubuntu 14.04.5 on aws
> mesos 1.0.1
> Java 1.7.0_111, openjdk
> Reporter: Luke Miner
>
> I'm trying to read in some json, infer a schema, and write it out again as parquet to s3 (s3a). For some reason, about a third of the way through the writing portion of the run, spark always errors out with the error included below.
> I can't find any obvious reasons for the issue:
> - it isn't out of memory and I have tried increasing the overhead memory
> - there are no long GC pauses.
> - There don't seem to be any additional error messages in the logs of the individual executors.
> - This does not appear to be a problem with badly formed json or corrupted files. I have unzipped and read in each file individually with no error.
> The script runs fine on another set of data that I have, which is of a very similar structure, but several orders of magnitude smaller.
> I am using the FileOutputCommitter. The algorithm version doesn't seem to matter.
> Here's a simplified version of the script:
> {code}
> object Foo {
> def parseJson(json: String): Option[Map[String, Any]] = {
> if (json == null)
> Some(Map())
> else
> parseOpt(json).map((j: JValue) => j.values.asInstanceOf[Map[String, Any]])
> }
> }
> }
> // read in as text and parse json using json4s
> val jsonRDD: RDD[String] = sc.textFile(inputPath)
> .map(row -> Foo.parseJson(row))
> // infer a schema that will encapsulate the most rows in a sample of size sampleRowNum
> val schema: StructType = Infer.getMostCommonSchema(sc, jsonRDD, sampleRowNum)
> // get documents compatibility with schema
> val jsonWithCompatibilityRDD: RDD[(String, Boolean)] = jsonRDD
> .map(js => (js, Infer.getSchemaCompatibility(schema, Infer.inferSchema(js)).toBoolean))
> .repartition(partitions)
> val jsonCompatibleRDD: RDD[String] = jsonWithCompatibilityRDD
> .filter { case (js: String, compatible: Boolean) => compatible }
> .map { case (js: String, _: Boolean) => js }
> // create a dataframe from documents with compatible schema
> val dataFrame: DataFrame = spark.read.schema(schema).json(jsonCompatibleRDD)
> dataFrame.write.parquet("s3a://foo/foo")
> {code}
> It completes the earlier schema inferring steps successfully. The error itself occurs on the last line, but I suppose that could encompass at least the immediately preceding statement, if not earlier:
> {code}
> org.apache.spark.SparkException: Task failed while writing rows
> at org.apache.spark.sql.execution.datasources.DefaultWriterContainer.writeRows(WriterContainer.scala:261)
> at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand$$anonfun$run$1$$anonfun$apply$mcV$sp$1.apply(InsertIntoHadoopFsRelationCommand.scala:143)
> at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand$$anonfun$run$1$$anonfun$apply$mcV$sp$1.apply(InsertIntoHadoopFsRelationCommand.scala:143)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
> at org.apache.spark.scheduler.Task.run(Task.scala:86)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.lang.RuntimeException: Failed to commit task
> at org.apache.spark.sql.execution.datasources.DefaultWriterContainer.org$apache$spark$sql$execution$datasources$DefaultWriterContainer$$commitTask$1(WriterContainer.scala:275)
> at org.apache.spark.sql.execution.datasources.DefaultWriterContainer$$anonfun$writeRows$1.apply$mcV$sp(WriterContainer.scala:257)
> at org.apache.spark.sql.execution.datasources.DefaultWriterContainer$$anonfun$writeRows$1.apply(WriterContainer.scala:252)
> at org.apache.spark.sql.execution.datasources.DefaultWriterContainer$$anonfun$writeRows$1.apply(WriterContainer.scala:252)
> at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1345)
> at org.apache.spark.sql.execution.datasources.DefaultWriterContainer.writeRows(WriterContainer.scala:258)
> ... 8 more
> Suppressed: java.lang.NullPointerException
> at org.apache.parquet.hadoop.InternalParquetRecordWriter.flushRowGroupToStore(InternalParquetRecordWriter.java:147)
> at org.apache.parquet.hadoop.InternalParquetRecordWriter.close(InternalParquetRecordWriter.java:113)
> at org.apache.parquet.hadoop.ParquetRecordWriter.close(ParquetRecordWriter.java:112)
> at org.apache.spark.sql.execution.datasources.parquet.ParquetOutputWriter.close(ParquetFileFormat.scala:569)
> at org.apache.spark.sql.execution.datasources.DefaultWriterContainer.org$apache$spark$sql$execution$datasources$DefaultWriterContainer$$abortTask$1(WriterContainer.scala:282)
> at org.apache.spark.sql.execution.datasources.DefaultWriterContainer$$anonfun$writeRows$2.apply$mcV$sp(WriterContainer.scala:258)
> at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1354)
> ... 9 more
> Caused by: com.amazonaws.AmazonClientException: Unable to unmarshall response (Failed to parse XML document with handler class com.amazonaws.services.s3.model.transform.XmlResponsesSaxParser$ListBucketHandler). Response Code: 200, Response Text: OK
> at com.amazonaws.http.AmazonHttpClient.handleResponse(AmazonHttpClient.java:738)
> at com.amazonaws.http.AmazonHttpClient.executeHelper(AmazonHttpClient.java:399)
> at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:232)
> at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:3528)
> at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:3480)
> at com.amazonaws.services.s3.AmazonS3Client.listObjects(AmazonS3Client.java:604)
> at org.apache.hadoop.fs.s3a.S3AFileSystem.getFileStatus(S3AFileSystem.java:962)
> at org.apache.hadoop.fs.s3a.S3AFileSystem.deleteUnnecessaryFakeDirectories(S3AFileSystem.java:1147)
> at org.apache.hadoop.fs.s3a.S3AFileSystem.finishedWrite(S3AFileSystem.java:1136)
> at org.apache.hadoop.fs.s3a.S3AOutputStream.close(S3AOutputStream.java:142)
> at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:72)
> at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:106)
> at org.apache.parquet.hadoop.ParquetFileWriter.end(ParquetFileWriter.java:400)
> at org.apache.parquet.hadoop.InternalParquetRecordWriter.close(InternalParquetRecordWriter.java:117)
> at org.apache.parquet.hadoop.ParquetRecordWriter.close(ParquetRecordWriter.java:112)
> at org.apache.spark.sql.execution.datasources.parquet.ParquetOutputWriter.close(ParquetFileFormat.scala:569)
> at org.apache.spark.sql.execution.datasources.DefaultWriterContainer.org$apache$spark$sql$execution$datasources$DefaultWriterContainer$$commitTask$1(WriterContainer.scala:267)
> ... 13 more
> Caused by: com.amazonaws.AmazonClientException: Failed to parse XML document with handler class com.amazonaws.services.s3.model.transform.XmlResponsesSaxParser$ListBucketHandler
> at com.amazonaws.services.s3.model.transform.XmlResponsesSaxParser.parseXmlInputStream(XmlResponsesSaxParser.java:150)
> at com.amazonaws.services.s3.model.transform.XmlResponsesSaxParser.parseListBucketObjectsResponse(XmlResponsesSaxParser.java:279)
> at com.amazonaws.services.s3.model.transform.Unmarshallers$ListObjectsUnmarshaller.unmarshall(Unmarshallers.java:75)
> at com.amazonaws.services.s3.model.transform.Unmarshallers$ListObjectsUnmarshaller.unmarshall(Unmarshallers.java:72)
> at com.amazonaws.services.s3.internal.S3XmlResponseHandler.handle(S3XmlResponseHandler.java:62)
> at com.amazonaws.services.s3.internal.S3XmlResponseHandler.handle(S3XmlResponseHandler.java:31)
> at com.amazonaws.http.AmazonHttpClient.handleResponse(AmazonHttpClient.java:712)
> ... 29 more
> Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 2; XML document structures must start and end within the same entity.
> at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
> at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
> at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
> at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
> at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
> at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.endEntity(Unknown Source)
> at org.apache.xerces.impl.XMLDocumentScannerImpl.endEntity(Unknown Source)
> at org.apache.xerces.impl.XMLEntityManager.endEntity(Unknown Source)
> at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
> at org.apache.xerces.impl.XMLEntityScanner.skipChar(Unknown Source)
> at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
> at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> at com.amazonaws.services.s3.model.transform.XmlResponsesSaxParser.parseXmlInputStream(XmlResponsesSaxParser.java:141)
> ... 35 more
> {code}
> Here's my conf:
> {code}
> spark.executor.extraJavaOptions -XX:+UseG1GC -XX:MaxPermSize=1G -XX:+HeapDumpOnOutOfMemoryError
> spark.executor.memory 16G
> spark.executor.uri https://foo/spark-2.0.1-bin-hadoop2.7.tgz
> spark.hadoop.fs.s3a.impl org.apache.hadoop.fs.s3a.S3AFileSystem
> spark.hadoop.fs.s3a.buffer.dir /raid0/spark
> spark.hadoop.fs.s3n.buffer.dir /raid0/spark
> spark.hadoop.fs.s3a.connection.timeout 500000
> spark.hadoop.fs.s3n.multipart.uploads.enabled true
> spark.hadoop.mapreduce.fileoutputcommitter.algorithm.version 2
> spark.hadoop.parquet.block.size 2147483648
> spark.hadoop.parquet.enable.summary-metadata false
> spark.jars.packages com.databricks:spark-avro_2.11:3.0.1,com.amazonaws:aws-java-sdk-pom:1.10.34
> spark.local.dir /raid0/spark
> spark.mesos.executor.memoryOverhead 4000
> spark.mesos.coarse false
> spark.mesos.constraints priority:1
> spark.network.timeout 600
> spark.rpc.message.maxSize 500
> spark.speculation false
> spark.sql.parquet.mergeSchema false
> spark.sql.planner.externalSort true
> spark.submit.deployMode client
> spark.task.cpus 1
> {code}
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