Scala Object Serialization - scala

I am having trouble opening multiple objects that were serialized into a single .bin file. Right now, I can only get one object to be read in when I attempt to open the file. After the first object is read, the error message is displayed (and no further objects are read). My code looks like the following:
val ois = new ObjectInputStream(new BufferedInputStream(newFileInputStream(chooser.selectedFile)))
val toRead:Int = ois.readInt()
for (i <- 0 to toRead) {
ois.readObject() match {
case anObject : myObject =>
aMutableBuffer += anObject
case _ =>
}
ois.close()
}
The error that I am getting is a lot of the following:
Exception in thread "AWT-EventQueue-0" java.security.PrivilegedActionException:java.security.PrivilegedActionException: java.io.IOException: Stream closed
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.security.PrivilegedActionException: java.io.IOException: Stream closed
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:652)
at java.awt.EventQueue$2.run(EventQueue.java:650)
... 9 more
Caused by: java.io.IOException: Stream closed
at java.io.BufferedInputStream.getBufIfOpen(BufferedInputStream.java:145)
at java.io.BufferedInputStream.read(BufferedInputStream.java:241)
at java.io.ObjectInputStream$PeekInputStream.peek(ObjectInputStream.java:2248)
at java.io.ObjectInputStream$BlockDataInputStream.peek(ObjectInputStream.java:2541)
at java.io.ObjectInputStream$BlockDataInputStream.peekByte(ObjectInputStream.java:2551)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1296)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:350)
atABCk.PhotoshopApp$$anonfun$ABCPhotoshopApp$$fileOpenPicture$1.apply$mcVI$sp(PhotoshopApp.scala:32)
at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:75)
at ABC.PhotoshopApp$.ABC$PhotoshopApp$$fileOpenPicture(PhotoshopApp.scala:31)
at ABC.PhotoshopApp$$anon$9$$anon$11$$anon$1$$anonfun$2.apply$mcV$sp(PhotoshopApp.scala:111)
at scala.swing.Action$$anon$2.apply(Action.scala:60)
at scala.swing.Action$$anon$1.actionPerformed(Action.scala:78)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.menuDragMouseReleased(BasicMenuItemUI.java:913)
at javax.swing.JMenuItem.fireMenuDragMouseReleased(JMenuItem.java:568)
at javax.swing.JMenuItem.processMenuDragMouseEvent(JMenuItem.java:465)
at javax.swing.JMenuItem.processMouseEvent(JMenuItem.java:411)
at javax.swing.MenuSelectionManager.processMouseEvent(MenuSelectionManager.java:305)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:852)
at java.awt.Component.processMouseEvent(Component.java:6373)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6138)
at java.awt.Container.processEvent(Container.java:2085)
at java.awt.Component.dispatchEventImpl(Component.java:4735)
at java.awt.Container.dispatchEventImpl(Container.java:2143)
at java.awt.Component.dispatchEvent(Component.java:4565)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
at java.awt.Container.dispatchEventImpl(Container.java:2129)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4565)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
... 14 more
This only happens when I read in an object to my buffer that keeps track of the objects. Moreover, I am able to save the file correctly (as I have done tests to ensure everything got there). Anyone have any ideas what is going on here?

You are closing your Stream ois at the end, but inside the loop. Then you try to read from it on the first line of the loop. Which obviously failes with a IOException: Stream closed

Related

pyspark on emr with boto3, copy of s3 object result with Futures timed out after [100000 milliseconds]

I have a pyspark application that will transform csv to parquet and before this happen I'm copying some S3 object from a bucket to another.
pyspark with spark 2.4, emr 5.27, maximizeResourceAllocation set to true
I have various csv files size, from 80kb to 500mb.
Nonetheless, my EMR cluster (it doesn't fail on local with spark-submit) fails at 70% completion on a file that is 166mb (a previous at 480mb succeeded).
The job is simple:
def organise_adwords_csv():
s3 = boto3.resource('s3')
bucket = s3.Bucket(S3_ORIGIN_RAW_BUCKET)
for obj in bucket.objects.filter(Prefix=S3_ORIGIN_ADWORDS_RAW + "/"):
key = obj.key
copy_source = {
'Bucket': S3_ORIGIN_RAW_BUCKET,
'Key': key
}
key_tab = obj.key.split("/")
if len(key_tab) < 5:
print("continuing from length", obj)
continue
file_name = ''.join(key_tab[len(key_tab)-1:len(key_tab)])
if file_name == '':
print("continuing", obj)
continue
table = file_name.split("_")[1].replace("-", "_")
new_path = "{0}/{1}/{2}".format(S3_DESTINATION_ORDERED_ADWORDS_RAW_PATH, table, file_name)
print("new_path", new_path) <- the last print will end here
try:
s3.meta.client.copy(copy_source, S3_DESTINATION_RAW_BUCKET, new_path)
print("copy done")
except Exception as e:
print(e)
print("an exception occured while copying")
if __name__=='__main__':
organise_adwords_csv()
print("copy Final done") <- never printed
spark = SparkSession.builder.appName("adwords_transform") \
...
but, in the stdout, no errors / exception are showing.
In stderr logs:
19/10/09 16:16:57 INFO ApplicationMaster: Waiting for spark context initialization...
19/10/09 16:18:37 ERROR ApplicationMaster: Uncaught exception:
java.util.concurrent.TimeoutException: Futures timed out after [100000 milliseconds]
at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:223)
at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:227)
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:220)
at org.apache.spark.deploy.yarn.ApplicationMaster.runDriver(ApplicationMaster.scala:468)
at org.apache.spark.deploy.yarn.ApplicationMaster.org$apache$spark$deploy$yarn$ApplicationMaster$$runImpl(ApplicationMaster.scala:305)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anonfun$run$1.apply$mcV$sp(ApplicationMaster.scala:245)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anonfun$run$1.apply(ApplicationMaster.scala:245)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anonfun$run$1.apply(ApplicationMaster.scala:245)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anon$3.run(ApplicationMaster.scala:779)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1844)
at org.apache.spark.deploy.yarn.ApplicationMaster.doAsUser(ApplicationMaster.scala:778)
at org.apache.spark.deploy.yarn.ApplicationMaster.run(ApplicationMaster.scala:244)
at org.apache.spark.deploy.yarn.ApplicationMaster$.main(ApplicationMaster.scala:803)
at org.apache.spark.deploy.yarn.ApplicationMaster.main(ApplicationMaster.scala)
19/10/09 16:18:37 INFO ApplicationMaster: Final app status: FAILED, exitCode: 13, (reason: Uncaught exception: java.util.concurrent.TimeoutException: Futures timed out after [100000 milliseconds]
at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:223)
at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:227)
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:220)
at org.apache.spark.deploy.yarn.ApplicationMaster.runDriver(ApplicationMaster.scala:468)
at org.apache.spark.deploy.yarn.ApplicationMaster.org$apache$spark$deploy$yarn$ApplicationMaster$$runImpl(ApplicationMaster.scala:305)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anonfun$run$1.apply$mcV$sp(ApplicationMaster.scala:245)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anonfun$run$1.apply(ApplicationMaster.scala:245)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anonfun$run$1.apply(ApplicationMaster.scala:245)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anon$3.run(ApplicationMaster.scala:779)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1844)
at org.apache.spark.deploy.yarn.ApplicationMaster.doAsUser(ApplicationMaster.scala:778)
at org.apache.spark.deploy.yarn.ApplicationMaster.run(ApplicationMaster.scala:244)
at org.apache.spark.deploy.yarn.ApplicationMaster$.main(ApplicationMaster.scala:803)
at org.apache.spark.deploy.yarn.ApplicationMaster.main(ApplicationMaster.scala)
)
19/10/09 16:18:37 INFO ShutdownHookManager: Shutdown hook called
I'm completely blind, I don't understand what is failing / why.
How can I figure that out? On local it works like a charm (but super slow of course)
Edit:
After many tries I can confirm that the function:
s3.meta.client.copy(copy_source, S3_DESTINATION_RAW_BUCKET, new_path)
make the EMR cluster timeout, even tho it processed 80% of the files already.
Does anyone have a recommendation about this?
s3.meta.client.copy(copy_source, S3_DESTINATION_RAW_BUCKET, new_path)
This will fail for any source object larger than 5 GB. please use multipart upload in AWS. See https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/s3.html#multipartupload

Flink: ERROR parse numeric value format

I'm trying to develop a K-means model in Flink (Scala), using Zeppelin.
This is part of my simple code:
//Reading data
val mapped : DataSet[Vector] = data.map {x => DenseVector (x._1,x._2) }
//Create algorithm
val knn = KNN()
.setK(3)
.setBlocks(10)
.setDistanceMetric(SquaredEuclideanDistanceMetric())
.setUseQuadTree(false)
.setSizeHint(CrossHint.SECOND_IS_SMALL)
...
//Just to learn I use the same data predicting the model
val result = knn.predict(mapped).collect()
When I print the data or to use predict method, i got this ERROR:
org.apache.flink.client.program.ProgramInvocationException: The program execution failed: Job execution failed.
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:409)
at org.apache.flink.client.program.StandaloneClusterClient.submitJob(StandaloneClusterClient.java:95)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:382)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:369)
at org.apache.flink.client.program.ClusterClient.run(ClusterClient.java:344)
at org.apache.flink.client.RemoteExecutor.executePlanWithJars(RemoteExecutor.java:211)
at org.apache.flink.client.RemoteExecutor.executePlan(RemoteExecutor.java:188)
at org.apache.flink.api.java.RemoteEnvironment.execute(RemoteEnvironment.java:172)
at org.apache.flink.api.java.ExecutionEnvironment.execute(ExecutionEnvironment.java:896)
at org.apache.flink.api.scala.ExecutionEnvironment.execute(ExecutionEnvironment.scala:637)
at org.apache.flink.api.scala.DataSet.collect(DataSet.scala:547)
... 36 elided
Caused by: org.apache.flink.runtime.client.JobExecutionException: Job execution failed.
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply$mcV$sp(JobManager.scala:822)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply(JobManager.scala:768)
at org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1$$anonfun$applyOrElse$7.apply(JobManager.scala:768)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:401)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.pollAndExecAll(ForkJoinPool.java:1253)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1346)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: org.apache.flink.api.common.io.ParseException: Line could not be parsed: '-6.59 -44.68'
ParserError NUMERIC_VALUE_FORMAT_ERROR
Expect field types: class java.lang.Double, class java.lang.Double
in file: /home/borja/flink/kmeans/points
at org.apache.flink.api.common.io.GenericCsvInputFormat.parseRecord(GenericCsvInputFormat.java:407)
at org.apache.flink.api.java.io.CsvInputFormat.readRecord(CsvInputFormat.java:110)
at org.apache.flink.api.common.io.DelimitedInputFormat.nextRecord(DelimitedInputFormat.java:470)
at org.apache.flink.api.java.io.CsvInputFormat.nextRecord(CsvInputFormat.java:78)
at org.apache.flink.runtime.operators.DataSourceTask.invoke(DataSourceTask.java:162)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:585)
at java.lang.Thread.run(Thread.java:748)
I do not know if it's my fault loading the data or it has related with something like that.
Thanks for any help! :)
You haven't shown us the code you are using to read and parse the data, which is where the error is occurring. But given the error message, I'll hazard a guess that you are using readCSVFile with data that is delimited by spaces or tabs, and didn't specify the fieldDelimiter (which defaults to comma). If that's the case, see the docs for how to configure the CSV parser.

spark: SAXParseException while writing to parquet on s3

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; there are no long GC pauses. There don't seem to be any additional error messages in the logs of the individual executors.
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 running spark 2.0.1-hadoop-2.7 and am using the FileOutputCommitter. The algorithm version doesn't seem to matter.
Edit:
This does not appear to be a problem in badly formed json or corrupted files. I have unzipped and read in each file individually with no error.
Here's a simplified version of the script:
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)
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 statemnt, if not earlier:
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
Here's my conf:
spark.executor.extraJavaOptions -XX:+UseG1GC -XX:MaxPermSize=1G -XX:+HeapDumpOnOutOfMemoryError
spark.executor.memory 16G
spark.executor.uri https://s3.amazonaws.com/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.parquet.block.size 2147483648
spark.hadoop.parquet.enable.summary-metadata false
spark.jars.packages com.databricks:spark-avro_2.11:3.0.1
spark.local.dir /raid0/spark
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
I can think for three possible reasons for this problem.
JVM version. AWS SDK checks for the following ones. "1.6.0_06",
"1.6.0_13", "1.6.0_17", "1.6.0_65", "1.7.0_45". If you are using one
of them, try upgrading.
Old AWS SDK. Refer to
https://github.com/aws/aws-sdk-java/issues/460 for a workaround.
If you lots of files in the directory where you are writing these files, you might be hitting https://issues.apache.org/jira/browse/HADOOP-13164. Consider increasing the timeout to larger values.
A SAXParseException may indicate a badly formatted XML file. Since the job fails roughly a third of the way through consistently, this means it's probably failing in the same place every time (a file whose partition is roughly a third of the way through the partition list).
Can you paste your script? It may be possible to wrap the Spark step in a try/catch loop that will print out the file if this error occurs, which will let you easily zoom in on the problem.
From the logs:
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 2; XML document structures must start and end within the same entity.
and
Caused by: com.amazonaws.AmazonClientException: Failed to parse XML document with handler class com.amazonaws.services.s3.model.transform.XmlResponsesSaxParser$ListBucketHandler
It looks like you have a corrupted/incorrectly formatted file, and your error is actually occurring during the read portion of the task. You could confirm this by trying another operation that will force the read such as count().
If confirmed, the goal would then be to find the corrupted file. You could do this by listing the s3 files, sc.parallelize() that list, and then trying to read the files in a custom function using map().
import boto3
from pyspark.sql import Row
def scanKeys(startKey, endKey):
bucket = boto3.resource('s3').Bucket('bucketName')
for obj in bucket.objects.filter(Prefix='prefix', Marker=startKey):
if obj.key < endKey:
yield obj.key
else:
return
def testFile(s3Path):
s3obj = boto3.resource('s3').Object(bucket_name='bucketName', key=key)
body = s3obj.get()['Body']
...
logic to test file format, or use a try/except and attempt to parse it
...
if fileFormatedCorrectly == True:
return Row(status='Good', key = s3Path)
else:
return Row(status='Fail', key = s3Path)
keys = list(scanKeys(startKey, endKey))
keyListRdd = sc.parallelize(keys, 1000)
keyListRdd.map(testFile).filter(lambda x: x.asDict.get('status') == 'Fail').collect()
This will return the s3 paths for the incorrectly formatted files
For Googlers:
If you:
have a versioned bucket
use s3a://
see ListBucketHandler and listObjects in your error message
Quick solution:
use s3:// instead of s3a://, which will use S3 driver provided by EMR
You may see this error because s3a:// in older versions uses S3::ListObjects (v1) API instead of S3::ListObjectsV2. The former would return extra info like owner, and is not robust against large number of deletion markers. Newer versions of the s3a:// driver solved this problem, but you could always use the s3:// driver instead.
Quote:
the V1 list API experience always returns 5000 entries (as set in fs.s3a.paging.maximum
except for the final entry
if you have versioning turned on in your bucket, deleted entries retain tombstone markers with references to their versions
which will surface in the S3-side of list calls, but get stripped out from the response
so...for a very large tree, you may end up S3 having to keep a channel open while is skips of thousands to millions of deleted
objects before it can find actual ones to return.
which can time out connections.
Quote:
Introducing a new version of the ListObjects (ListObjectsV2) API that allows listing objects with a large number of delete markers.
Quote:
If there are thousands of delete markers, the list operation might timeout。

mongodb allanbank async driver callback being called twice

I have a simple callback bound to a findAsync call. Every few requests I observe a failure even though the data in the database is static.
Some quick debugging shows that my callback is ALWAYS being called twice. The cases where my app fails are caused by a null MongoIterator<Document> being passed in to my callback. Of course I only expected a single callback when the data is ready (or if there was an exception).
Is this expected behavior? Is there something I can do to ensure my callback is only called once when the query is complete?
Here is the code snippet:
collection.findAsync(
[
callback: { MongoIterator<Document> v ->
List data = []
try {
while(v.hasNext()) {
data.add(docToJson(v.next()))
}
} finally {
if (v != null) v.close()
}
sendReply([ status: 'ok', data: data ])
},
exception: { Throwable t ->
sendReply([ status: 'error', message: t.message ])
}
] as Callback<MongoIterator<Document>>,
find
)
Here is the stack trace:
Unexpected MongoDB Connection closed: Auth(MongoDB(43026-->localhost/127.0.0.1:27017)). Will try to reconnect.
Reconnected to localhost/127.0.0.1:27017
Exception in thread "MongoDB 43026<--localhost/127.0.0.1:27017" java.lang.NullPointerException: Cannot invoke method hasNext() on null object
at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:77)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:45)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
at org.codehaus.groovy.runtime.callsite.NullCallSite.call(NullCallSite.java:32)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:54)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:112)
at mongoAsync$_run_closure2_closure6.doCall(mongoAsync.groovy:126)
at sun.reflect.GeneratedMethodAccessor54.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:233)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:272)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:909)
at groovy.lang.Closure.call(Closure.java:411)
at org.codehaus.groovy.runtime.ConvertedMap.invokeCustom(ConvertedMap.java:50)
at org.codehaus.groovy.runtime.ConversionHandler.invoke(ConversionHandler.java:81)
at com.sun.proxy.$Proxy14.callback(Unknown Source)
at com.allanbank.mongodb.client.AbstractReplyCallback.handle(AbstractReplyCallback.java:82)
at com.allanbank.mongodb.client.AbstractValidatingReplyCallback.callback(AbstractValidatingReplyCallback.java:72)
at com.allanbank.mongodb.client.AbstractValidatingReplyCallback.callback(AbstractValidatingReplyCallback.java:33)
at com.allanbank.mongodb.connection.message.ReplyHandler.reply(ReplyHandler.java:77)
at com.allanbank.mongodb.connection.socket.SocketConnection.reply(SocketConnection.java:560)
at com.allanbank.mongodb.connection.socket.SocketConnection$ReceiveRunnable.receiveOne(SocketConnection.java:735)
at com.allanbank.mongodb.connection.socket.SocketConnection$ReceiveRunnable.run(SocketConnection.java:683)
at java.lang.Thread.run(Thread.java:722)
Thanks for the extra information.
I am pretty sure I found the bug.
There is a race between the callback/iterator for the query getting the name of the server handling the query (needed for the GetMore requests) and the receive of a reply. Not sure how it has not been seen by others.
There is a patched jar here: [redact]. Let me know if it solves the problem for you.
The 1.2.2 version is available with the fix: http://www.allanbank.com/mongodb-async-driver/download.html
Assuming it does, I will push this fix out as a 1.2.2 tomorrow.
Rob.
Edit: Add link to official version.

Casbah's problem with large number of returned objects

Casbah (or the java driver for mongodb) seems to have problem dealing with a large number of returned objects. For example, the following code segment would produce an IllegalArgumentException and won't return a single result (full stack trace below). However, if I reduce the "limit(...)" to 1994, everything seems to work fine.
for (link <- links; query = link $exists true) {
val group = new HashMap[String, Set[(String, String)]] with MultiMap[String, (String, String)]
log.find(query, fieldsToGet.result).limit(1996) foreach {
x => {
group.addBinding(x.get(link).toString, (x.get("_id").toString(), x.get("eventType").toString))
}
}
allGroups += link -> group
}
Apr 26, 2011 8:23:40 PM com.mongodb.DBTCPConnector$MyPort error
SEVERE: MyPort.error called
java.lang.IllegalArgumentException: response too long: 1278031173
at com.mongodb.Response.<init>(Response.java:40)
at com.mongodb.DBPort.go(DBPort.java:101)
at com.mongodb.DBPort.go(DBPort.java:66)
at com.mongodb.DBPort.call(DBPort.java:56)
at com.mongodb.DBTCPConnector.call(DBTCPConnector.java:211)
at com.mongodb.DBApiLayer$MyCollection.__find(DBApiLayer.java:266)
at com.mongodb.DBCursor._check(DBCursor.java:309)
at com.mongodb.DBCursor._hasNext(DBCursor.java:431)
at com.mongodb.DBCursor.hasNext(DBCursor.java:456)
at com.mongodb.casbah.MongoCursorBase$class.hasNext(MongoCursor.scala:72)
at com.mongodb.casbah.MongoCursor.hasNext(MongoCursor.scala:517)
at scala.collection.Iterator$class.foreach(Iterator.scala:631)
at com.mongodb.casbah.MongoCursor.foreach(MongoCursor.scala:517)
at Sequencer$$anonfun$3.apply(Sequencer.scala:23)
at Sequencer$$anonfun$3.apply(Sequencer.scala:20)
at scala.collection.LinearSeqOptimized$class.foreach(LinearSeqOptimized.scala:61)
at scala.collection.immutable.List.foreach(List.scala:45)
at Sequencer$.<init>(Sequencer.scala:20)
at Sequencer$.<clinit>(Sequencer.scala)
at Sequencer.main(Sequencer.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:115)
Exception in thread "main" java.lang.ExceptionInInitializerError
at Sequencer.main(Sequencer.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.intellij.rt.execution.application.AppMain.main(AppMain.java:115)
Caused by: java.lang.IllegalArgumentException: response too long: 1278031173
at com.mongodb.Response.<init>(Response.java:40)
at com.mongodb.DBPort.go(DBPort.java:101)
at com.mongodb.DBPort.go(DBPort.java:66)
at com.mongodb.DBPort.call(DBPort.java:56)
at com.mongodb.DBTCPConnector.call(DBTCPConnector.java:211)
at com.mongodb.DBApiLayer$MyCollection.__find(DBApiLayer.java:266)
at com.mongodb.DBCursor._check(DBCursor.java:309)
at com.mongodb.DBCursor._hasNext(DBCursor.java:431)
at com.mongodb.DBCursor.hasNext(DBCursor.java:456)
at com.mongodb.casbah.MongoCursorBase$class.hasNext(MongoCursor.scala:72)
at com.mongodb.casbah.MongoCursor.hasNext(MongoCursor.scala:517)
at scala.collection.Iterator$class.foreach(Iterator.scala:631)
at com.mongodb.casbah.MongoCursor.foreach(MongoCursor.scala:517)
at Sequencer$$anonfun$3.apply(Sequencer.scala:23)
at Sequencer$$anonfun$3.apply(Sequencer.scala:20)
at scala.collection.LinearSeqOptimized$class.foreach(LinearSeqOptimized.scala:61)
at scala.collection.immutable.List.foreach(List.scala:45)
at Sequencer$.<init>(Sequencer.scala:20)
at Sequencer$.<clinit>(Sequencer.scala)
... 6 more
Seems the exception was produced by the following check in the "Response.java" in the java driver.
ByteArrayInputStream bin = new ByteArrayInputStream( b );
_len = Bits.readInt( bin );
if ( _len > ( 32 * 1024 * 1024 ) )
throw new IllegalArgumentException( "response too long: " + _len );
Could it be caused by that particular object returned? or could this be about casbah?
Thanks,
Derek
It looks like the Java driver is checking to see if the current response block is greater than 32 Megabytes and then throwing the exception.
If you set the batchSize(FEWER_NUMBER_OF_DOCS) on the cursor, this will reduce the lock time in the database and return less than 32 MB worth of data.
I would play around with the batchSize to see what is optimal for your application.
http://api.mongodb.org/scala/casbah/2.1.2/scaladoc/
The max should probably be increased in the Java driver.
The strange part about your response is that it says it is returning ~ 1.19 GB worth of data.
If your response doesn't have that much data, it may indicate the collection is corrupt.