I have a really simple PySpark script that creates a dataframe from some parquet data on S3 and then call count() method and print out the number of records.
I run the script on AWS EMR cluster and I'm seeing following strange WARN information:
17/12/04 14:20:26 WARN ServletHandler:
javax.servlet.ServletException: java.util.NoSuchElementException: None.get
at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:489)
at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
at org.spark_project.jetty.servlet.ServletHolder.handle(ServletHolder.java:845)
at org.spark_project.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1689)
at org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter.doFilter(AmIpFilter.java:164)
at org.spark_project.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676)
at org.spark_project.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:581)
at org.spark_project.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1180)
at org.spark_project.jetty.servlet.ServletHandler.doScope(ServletHandler.java:511)
at org.spark_project.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1112)
at org.spark_project.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.spark_project.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:461)
at org.spark_project.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:213)
at org.spark_project.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134)
at org.spark_project.jetty.server.Server.handle(Server.java:524)
at org.spark_project.jetty.server.HttpChannel.handle(HttpChannel.java:319)
at org.spark_project.jetty.server.HttpConnection.onFillable(HttpConnection.java:253)
at org.spark_project.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:273)
at org.spark_project.jetty.io.FillInterest.fillable(FillInterest.java:95)
at org.spark_project.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93)
at org.spark_project.jetty.util.thread.strategy.ExecuteProduceConsume.executeProduceConsume(ExecuteProduceConsume.java:303)
at org.spark_project.jetty.util.thread.strategy.ExecuteProduceConsume.produceConsume(ExecuteProduceConsume.java:148)
at org.spark_project.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:136)
at org.spark_project.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:671)
at org.spark_project.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:589)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.NoSuchElementException: None.get
at scala.None$.get(Option.scala:347)
at scala.None$.get(Option.scala:345)
at org.apache.spark.status.api.v1.MetricHelper.submetricQuantiles(AllStagesResource.scala:313)
at org.apache.spark.status.api.v1.AllStagesResource$$anon$1.build(AllStagesResource.scala:178)
at org.apache.spark.status.api.v1.AllStagesResource$.taskMetricDistributions(AllStagesResource.scala:181)
at org.apache.spark.status.api.v1.OneStageResource$$anonfun$taskSummary$1.apply(OneStageResource.scala:71)
at org.apache.spark.status.api.v1.OneStageResource$$anonfun$taskSummary$1.apply(OneStageResource.scala:62)
at org.apache.spark.status.api.v1.OneStageResource$$anonfun$withStageAttempt$1.apply(OneStageResource.scala:130)
at org.apache.spark.status.api.v1.OneStageResource$$anonfun$withStageAttempt$1.apply(OneStageResource.scala:126)
at org.apache.spark.status.api.v1.OneStageResource.withStage(OneStageResource.scala:97)
at org.apache.spark.status.api.v1.OneStageResource.withStageAttempt(OneStageResource.scala:126)
at org.apache.spark.status.api.v1.OneStageResource.taskSummary(OneStageResource.scala:62)
at sun.reflect.GeneratedMethodAccessor153.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:205)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102)
at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
... 28 more
17/12/04 14:20:26 WARN HttpChannel: //ip-172-31-81-10.ec2.internal:4040/api/v1/applications/application_1512395256824_0002/stages/3/0/taskSummary?proxyapproved=true
javax.servlet.ServletException: java.util.NoSuchElementException: None.get
at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:489)
at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
at org.spark_project.jetty.servlet.ServletHolder.handle(ServletHolder.java:845)
at org.spark_project.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1689)
at org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter.doFilter(AmIpFilter.java:164)
at org.spark_project.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676)
at org.spark_project.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:581)
at org.spark_project.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1180)
at org.spark_project.jetty.servlet.ServletHandler.doScope(ServletHandler.java:511)
at org.spark_project.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1112)
at org.spark_project.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.spark_project.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:461)
at org.spark_project.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:213)
at org.spark_project.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134)
at org.spark_project.jetty.server.Server.handle(Server.java:524)
at org.spark_project.jetty.server.HttpChannel.handle(HttpChannel.java:319)
at org.spark_project.jetty.server.HttpConnection.onFillable(HttpConnection.java:253)
at org.spark_project.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:273)
at org.spark_project.jetty.io.FillInterest.fillable(FillInterest.java:95)
at org.spark_project.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93)
at org.spark_project.jetty.util.thread.strategy.ExecuteProduceConsume.executeProduceConsume(ExecuteProduceConsume.java:303)
at org.spark_project.jetty.util.thread.strategy.ExecuteProduceConsume.produceConsume(ExecuteProduceConsume.java:148)
at org.spark_project.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:136)
at org.spark_project.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:671)
at org.spark_project.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:589)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.NoSuchElementException: None.get
at scala.None$.get(Option.scala:347)
at scala.None$.get(Option.scala:345)
at org.apache.spark.status.api.v1.MetricHelper.submetricQuantiles(AllStagesResource.scala:313)
at org.apache.spark.status.api.v1.AllStagesResource$$anon$1.build(AllStagesResource.scala:178)
at org.apache.spark.status.api.v1.AllStagesResource$.taskMetricDistributions(AllStagesResource.scala:181)
at org.apache.spark.status.api.v1.OneStageResource$$anonfun$taskSummary$1.apply(OneStageResource.scala:71)
at org.apache.spark.status.api.v1.OneStageResource$$anonfun$taskSummary$1.apply(OneStageResource.scala:62)
at org.apache.spark.status.api.v1.OneStageResource$$anonfun$withStageAttempt$1.apply(OneStageResource.scala:130)
at org.apache.spark.status.api.v1.OneStageResource$$anonfun$withStageAttempt$1.apply(OneStageResource.scala:126)
at org.apache.spark.status.api.v1.OneStageResource.withStage(OneStageResource.scala:97)
at org.apache.spark.status.api.v1.OneStageResource.withStageAttempt(OneStageResource.scala:126)
at org.apache.spark.status.api.v1.OneStageResource.taskSummary(OneStageResource.scala:62)
at sun.reflect.GeneratedMethodAccessor153.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:205)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102)
at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
It seems like it does not fail the job, though. I got the count returned successfully.
Just wonder if anyone know why this happens and how to get rid of it.
Thanks
Those warning messages can be suppressed by adding the following lines to /etc/spark/conf/log4j.properties:
log4j.logger.org.spark_project.jetty.server.HttpChannel=ERROR
log4j.logger.org.spark_project.jetty.servlet.ServletHandler=ERROR
I didn't see any impact on performance nor on job stability.
Now my logs are much readable :)
For those who use AWS EMR with Spark, I also got the same error message when executing my Spark jobs in
emr-5.10.0
emr-5.11.0
emr-5.11.1
emr-5.12.0
Simply downgrading to emr-5.9.0 will help you to solve this problem.
Hope it helps.
Related
I'm trying to use a multidelimiter in a table insert for a hive job in emr on amazon aws. As explained in this link. The delimiter for the file is "|".
https://cwiki.apache.org/confluence/display/Hive/MultiDelimitSerDe
However, I ended up having to use...
ROW FORMAT SERDE 'org.apache.hadoop.hive.contrib.serde2.MultiDelimitSerDe'
Instead of the documented...
ROW FORMAT SERDE 'org.apache.hadoop.hive.serde2.MultiDelimitSerDe'
in order for it to not give me this error.
FAILED: Execution Error, return code 1 from org.apache.hadoop.hive.ql.exec.DDLTask. Cannot validate serde: org.apache.hadoop.hive.serde2.MultiDelimitSerDe
OK. So when I don't get that error, by adding the .contrib, I get this error which is caused by Caused by: org.apache.hadoop.hive.ql.metadata.HiveException: java.lang.ClassNotFoundException: Class org.apache.hadoop.hive.contrib.serde2.MultiDelimitSerDe not found
Status: Failed
Vertex failed, vertexName=Map 1, vertexId=vertex_1548264520414_0027_1_00, diagnostics=[Task failed, taskId=task_1548264520414_0027_1_00_000021, diagnostics=[TaskAttempt 0 failed, info=[Error: Error while running task ( failure ) : attempt_1548264520414_0027_1_00_000021_0:java.lang.RuntimeException: java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:211)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.run(TezProcessor.java:168)
at org.apache.tez.runtime.LogicalIOProcessorRuntimeTask.run(LogicalIOProcessorRuntimeTask.java:370)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:73)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:61)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1840)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:61)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:37)
at org.apache.tez.common.CallableWithNdc.call(CallableWithNdc.java:36)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Map operator initialization failed
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:354)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:184)
... 14 more
Caused by: org.apache.hadoop.hive.ql.metadata.HiveException: java.lang.ClassNotFoundException: Class org.apache.hadoop.hive.contrib.serde2.MultiDelimitSerDe not found
at org.apache.hadoop.hive.ql.exec.MapOperator.getConvertedOI(MapOperator.java:328)
at org.apache.hadoop.hive.ql.exec.MapOperator.setChildren(MapOperator.java:420)
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.init(MapRecordProcessor.java:286)
... 15 more
So I've been reading that you have to add the .jar file.
https://community.hortonworks.com/questions/82189/hive-cannot-see-jar.html
And so I've tried all kinds of things to get this to work. It says that it is adding it it to the class path.
hive> add jar /usr/lib/hive/lib/hive-contrib-2.3.3-amzn-1.jar
> ;
Added [/usr/lib/hive/lib/hive-contrib-2.3.3-amzn-1.jar] to class path
Added resources: [/usr/lib/hive/lib/hive-contrib-2.3.3-amzn-1.jar]
hive> add jar /usr/lib/hive/lib/hive-contrib.jar
> ;
Added [/usr/lib/hive/lib/hive-contrib.jar] to class path
Added resources: [/usr/lib/hive/lib/hive-contrib.jar]
hive> exit;
So I'm not sure what to do. It's acting as if the .jar file for hive-contrib isn't in the class path despite me adding it. I've also tried running...
export HADOOP_USER_CLASSPATH_FIRST=true
which is found here...
How to include jars in Hive (Amazon Hadoop env)
And that doesn't fix it either.
How can I use a multidelimiter SerDe property for a hive job on aws?
Thank you.
I could not get MultiDelimitSerDe to work. Instead, I was lucky in that the delimiter had quotations on either side of the pipe. So it looks like "|". This turns the values between the quotes into strings, so the additional pipes in those column values don't act as delimiters.
"Test | Test2 "|" Test3 | Test 4 | Test 5 "|" Test 6 "
You can see an explanation in the link below. The part that talks about it is in the comments, not the article.
https://www.ericlin.me/2015/07/how-to-create-a-hive-multi-character-delimitered-table/
If I didn't have those quotation marks around the delimiter, I'm not sure how I would have been able to work with a multi delimiter. Especially if I had quotations in any of my fields, but after checking, out of the billions of rows, there is not a single quote.
For small s3 input files (~10GB), glue ETL job works fine but for the larger dataset (~200GB), the job is failing.
Adding a part of ETL code.
# Converting Dynamic frame to dataframe
df = dropnullfields3.toDF()
# create new partition column
partitioned_dataframe = df.withColumn('part_date', df['timestamp_utc'].cast('date'))
# store the data in parquet format on s3
partitioned_dataframe.write.partitionBy(['part_date']).format("parquet").save(output_lg_partitioned_dir, mode="append")
Job executed for 4 hours and threw error.
File "script_2017-11-23-15-07-32.py", line 49, in
partitioned_dataframe.write.partitionBy(['part_date']).format("parquet").save(output_lg_partitioned_dir,
mode="append") File
"/mnt/yarn/usercache/root/appcache/application_1511449472652_0001/container_1511449472652_0001_02_000001/pyspark.zip/pyspark/sql/readwriter.py",
line 550, in save File
"/mnt/yarn/usercache/root/appcache/application_1511449472652_0001/container_1511449472652_0001_02_000001/py4j-0.10.4-src.zip/py4j/java_gateway.py",
line 1133, in call File
"/mnt/yarn/usercache/root/appcache/application_1511449472652_0001/container_1511449472652_0001_02_000001/pyspark.zip/pyspark/sql/utils.py",
line 63, in deco File
"/mnt/yarn/usercache/root/appcache/application_1511449472652_0001/container_1511449472652_0001_02_000001/py4j-0.10.4-src.zip/py4j/protocol.py",
line 319, in get_return_value py4j.protocol.Py4JJavaError: An error
occurred while calling o172.save. : org.apache.spark.SparkException:
Job aborted. at
org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:147)
at
org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:121)
at
org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:121)
at
org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
at
org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:121)
at
org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:101)
at
org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58)
at
org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56)
at
org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:114)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:114)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:135)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at
org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:132)
at
org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:113)
at
org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:87)
at
org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:87)
at
org.apache.spark.sql.execution.datasources.DataSource.write(DataSource.scala:492)
at
org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:215)
at
org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:198)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498) at
py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at
py4j.Gateway.invoke(Gateway.java:280) at
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79) at
py4j.GatewayConnection.run(GatewayConnection.java:214) at
java.lang.Thread.run(Thread.java:748) Caused by:
org.apache.spark.SparkException: Job aborted due to stage failure:
Total size of serialized results of 3385 tasks (1024.1 MB) is bigger
than spark.driver.maxResultSize (1024.0 MB) at
org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
at
scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at
org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at scala.Option.foreach(Option.scala:257) at
org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48) at
org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918) at
org.apache.spark.SparkContext.runJob(SparkContext.scala:1931) at
org.apache.spark.SparkContext.runJob(SparkContext.scala:1951) at
org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:127)
... 30 more
End of LogType:stdout
I would appreciate it if you could provide any guidance to resolve this issue.
You can only set configurable options like maxResultSize during context instantiation, and glue provides you with a context (from memory you can't instantiate a new context). I don't think you will be able to change the value of this property.
You'll normally get this error if you collect results to the driver which exceed the specified size. You aren't doing that in this case so the error is confusing.
It seems like you are spawning 3385 tasks, which are presumably related to the dates in your input file (3385 dates, ~9 years?). You might try writing this file in batches, e.g.
partitioned_dataframe = df.withColumn('part_date', df['timestamp_utc'].cast('date'))
for year in range(2000,2018):
partitioned_dataframe = partitioned_dateframe.where(year(part_date) = year)
partitioned_dataframe.write.partitionBy(['part_date'])
.format("parquet")
.save(output_lg_partitioned_dir, mode="append")
I haven't checked this code; you'll at least need to import pyspark.sql.functions.year for it to work.
When I've done data processing with Glue I simply found that batching the work was more effective than trying to get large datasets be completed successfully. The system is good but hard to debug; the stability on large data doesn't come easily.
I am trying to import a JSON data from S3, and after making some queries, export the output as JSON format to S3 again. However, I get the "org.apache.hadoop.hive.serde2.SerDeException: java.io.IOException: Start token not found where expected" error at hive step on EMR cluster. In order to understand what the problem is, I simplify the Hive script and JSON data, but it keeps giving the same error. How can I solve this problem?
Cluster configuration:
Release: emr-5.3.1
Hive version: 2.1.1
Hadoop distribution: Amazon 2.7.3
Service Role: EMR_DefaultRole
MasterInstanceType: m4.large
The content of the simplifed JSON data:
[{"MyID":"FOO123","MyField":"FOO"},{"MyID":"BAR123","MyField":"BAR"}]
Hive script:
DROP TABLE IF EXISTS SOURCE;
DROP TABLE IF EXISTS DESTINATION;
CREATE EXTERNAL TABLE SOURCE(MyID STRING, MyField STRING)
ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'
LOCATION 's3://myPath/subPath/';
CREATE EXTERNAL TABLE DESTINATION(MyID STRING, MyField STRING)
ROW FORMAT SERDE 'org.apache.hive.hcatalog.data.JsonSerDe'
LOCATION 's3://anotherPath/subPath/';
INSERT OVERWRITE TABLE DESTINATION SELECT MyID, MyField FROM SOURCE;
And here is the stack trace:
Vertex failed, vertexName=Map 4, vertexId=vertex_1278452616863_0001_1_00, diagnostics=[Task failed, taskId=task_1278452616863, diagnostics=[TaskAttempt 0 failed, info=[Error: Error while running task ( failure ) : attempt_1278452616863:java.lang.RuntimeException: java.lang.RuntimeException: org.apache.hadoop.hive.ql.metadata.HiveException: Hive Runtime Error while processing writable [{"MyID":"FOO123","MyField":"FOO"},{"MyID":"BAR123","MyField":"BAR"}]
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:211)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.run(TezProcessor.java:168)
at org.apache.tez.runtime.LogicalIOProcessorRuntimeTask.run(LogicalIOProcessorRuntimeTask.java:370)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:73)
at org.apache.tez.runtime.task.TaskRunner2Callable$1.run(TaskRunner2Callable.java:61)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:422)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1698)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:61)
at org.apache.tez.runtime.task.TaskRunner2Callable.callInternal(TaskRunner2Callable.java:37)
at org.apache.tez.common.CallableWithNdc.call(CallableWithNdc.java:36)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: org.apache.hadoop.hive.ql.metadata.HiveException: Hive Runtime Error while processing writable [{"MyID":"FOO123","MyField":"FOO"},{"MyID":"BAR123","MyField":"BAR"}]
at org.apache.hadoop.hive.ql.exec.tez.MapRecordSource.processRow(MapRecordSource.java:95)
at org.apache.hadoop.hive.ql.exec.tez.MapRecordSource.pushRecord(MapRecordSource.java:70)
at org.apache.hadoop.hive.ql.exec.tez.MapRecordProcessor.run(MapRecordProcessor.java:383)
at org.apache.hadoop.hive.ql.exec.tez.TezProcessor.initializeAndRunProcessor(TezProcessor.java:185)
... 14 more
Caused by: org.apache.hadoop.hive.ql.metadata.HiveException: Hive Runtime Error while processing writable [{"MyID":"FOO123","MyField":"FOO"},{"MyID":"BAR123","MyField":"BAR"}]
at org.apache.hadoop.hive.ql.exec.MapOperator.process(MapOperator.java:497)
at org.apache.hadoop.hive.ql.exec.tez.MapRecordSource.processRow(MapRecordSource.java:86)
... 17 more
Caused by: org.apache.hadoop.hive.serde2.SerDeException: java.io.IOException: Start token not found where expected
at org.apache.hive.hcatalog.data.JsonSerDe.deserialize(JsonSerDe.java:183)
at org.apache.hadoop.hive.ql.exec.MapOperator$MapOpCtx.readRow(MapOperator.java:128)
at org.apache.hadoop.hive.ql.exec.MapOperator$MapOpCtx.access$200(MapOperator.java:92)
at org.apache.hadoop.hive.ql.exec.MapOperator.process(MapOperator.java:488)
... 18 more
Caused by: java.io.IOException: Start token not found where expected
at org.apache.hive.hcatalog.data.JsonSerDe.deserialize(JsonSerDe.java:169)
... 21 more
Thanks.
JSON should start with { and not with array ([)
I tried with this approach updated my JSON file with structure as
{"MyID":"FOO123","MyField":"FOO"},
{"MyID":"BAR123","MyField":"BAR"}
but after done, I noticed only the first object is being inserted into the table.
I am trying to execute sqoop job in biginsights. I am importing data from oracle db to hdfs. Below is the sqoop command which starts executing mapper and stops after sometime.
sudo sqoop import --connect "jdbc:oracle:thin:#(DESCRIPTION = (ADDRESS = (PROTOCOL = TCP)(HOST = ***.**.**.***)(PORT = 1908)) (CONNECT_DATA = (SERVER = DEDICATED) (SERVICE_NAME = GPRSDB1) ) )" --username **** --password ***** --query "select distinct pr_con_id from s_org_ext where \$CONDITIONS" --where "PAR_DIVN_ID ='1-1POG9V' AND rownum< 100" --target-dir /user/bigsql/crm/s_contact_mh --fields-terminated-by ',' --m 1
Below is the error :
Error: java.lang.RuntimeException: java.lang.RuntimeException: java.sql.SQLException: The Network Adapter could not establish the connection
at org.apache.sqoop.mapreduce.db.DBInputFormat.setConf(DBInputFormat.java:167)
at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:73)
at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:133)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:746)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:163)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:415)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1628)
at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)
Caused by: java.lang.RuntimeException: java.sql.SQLException: The Network Adapter could not establish the connection
at org.apache.sqoop.mapreduce.db.DBInputFormat.getConnection(DBInputFormat.java:220)
at org.apache.sqoop.mapreduce.db.DBInputFormat.setConf(DBInputFormat.java:165)
... 9 more
Caused by: java.sql.SQLException: The Network Adapter could not establish the connection
at oracle.jdbc.driver.SQLStateMapping.newSQLException(SQLStateMapping.java:70)
at oracle.jdbc.driver.DatabaseError.newSQLException(DatabaseError.java:133)
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:199)
at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:480)
at oracle.jdbc.driver.T4CConnection.logon(T4CConnection.java:413)
at oracle.jdbc.driver.PhysicalConnection.<init>(PhysicalConnection.java:508)
at oracle.jdbc.driver.T4CConnection.<init>(T4CConnection.java:203)
at oracle.jdbc.driver.T4CDriverExtension.getConnection(T4CDriverExtension.java:33)
at oracle.jdbc.driver.OracleDriver.connect(OracleDriver.java:510)
at java.sql.DriverManager.getConnection(DriverManager.java:571)
at java.sql.DriverManager.getConnection(DriverManager.java:215)
at org.apache.sqoop.mapreduce.db.DBConfiguration.getConnection(DBConfiguration.java:302)
at org.apache.sqoop.mapreduce.db.DBInputFormat.getConnection(DBInputFormat.java:213)
... 10 more
Caused by: oracle.net.ns.NetException: The Network Adapter could not establish the connection
at oracle.net.nt.ConnStrategy.execute(ConnStrategy.java:328)
at oracle.net.resolver.AddrResolution.resolveAndExecute(AddrResolution.java:421)
at oracle.net.ns.NSProtocol.establishConnection(NSProtocol.java:630)
at oracle.net.ns.NSProtocol.connect(NSProtocol.java:206)
at oracle.jdbc.driver.T4CConnection.connect(T4CConnection.java:966)
at oracle.jdbc.driver.T4CConnection.logon(T4CConnection.java:292)
... 18 more
Caused by: java.net.ConnectException: Connection timed out
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:579)
at java.net.Socket.connect(Socket.java:528)
at java.net.Socket.<init>(Socket.java:425)
at java.net.Socket.<init>(Socket.java:208)
at oracle.net.nt.TcpNTAdapter.connect(TcpNTAdapter.java:127)
at oracle.net.nt.ConnOption.connect(ConnOption.java:126)
at oracle.net.nt.ConnStrategy.execute(ConnStrategy.java:306)
... 23 more
Please help me out to solve this issue. Thanks in advance.
SQOOP Eval function just acts on the RDBMS database and returns you the resultset. Here hadoop does not come into picture.
SQOOP Import function tries to import the data from RDBMS and load it into HDFS. For Sqoop Import to work as desired the db server should be reachable from all nodes in the cluster.
I am trying to protect a Glassfish v3.0.0 with a J2EE agent (v3.3.0 and OpenAM server v9.5.3).
The installation and deployment was OK, but when I log in with a valid user I get some errors.
I don´t know if it is a compatibility problem, a GlassFish misconfiguration or another thing.
These are the error logs:
Browser error
Exceptions details : null
________________________________________
java.lang.NullPointerException at java.io.File.(File.java:222) at org.glassfish.webservices.monitoring.WebServiceTesterServlet.initializePort(WebServiceTesterServlet.java:505) at org.glassfish.webservices.monitoring.WebServiceTesterServlet.doGet(WebServiceTesterServlet.java:165) at org.glassfish.webservices.monitoring.WebServiceTesterServlet.invoke(WebServiceTesterServlet.java:100) at org.glassfish.webservices.JAXWSServlet.doGet(JAXWSServlet.java:193) at javax.servlet.http.HttpServlet.service(HttpServlet.java:734) at javax.servlet.http.HttpServlet.service(HttpServlet.java:847) at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1523) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:343) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:215) at com.sun.identity.agents.filter.AmAgentBaseFilter.allowRequestToContinue(AmAgentBaseFilter.java:128) at com.sun.identity.agents.filter.AmAgentBaseFilter.doFilter(AmAgentBaseFilter.java:78) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:277) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:188) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:641) at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:97) at com.sun.enterprise.web.PESessionLockingStandardPipeline.invoke(PESessionLockingStandardPipeline.java:85) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:185) at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:332) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:233) at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:165) at com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:791) at com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:693) at com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:954) at com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:170) at com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:135) at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:102) at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:88) at com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:76) at com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:53) at com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:57) at com.sun.grizzly.ContextTask.run(ContextTask.java:69) at com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:330) at com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:309) at java.lang.Thread.run(Thread.java:662)
**GlassFish Log**
[#|2014-08-05T16:15:29.109+0200|WARNING|glassfishv3.0|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=24;_ThreadName=http-thread-pool-8080-(1);|StandardWrapperValve[default]: PWC1406: Servlet.service() for servlet default threw exception
java.lang.ClassNotFoundException: com.sun.identity.agents.filter.AmAgentFilter
at org.glassfish.web.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:1985)
at org.glassfish.web.loader.WebappClassLoader.findClass(WebappClassLoader.java:888)
at org.glassfish.web.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1420)
at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:245)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:237)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:277)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:188)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:641)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:97)
at com.sun.enterprise.web.PESessionLockingStandardPipeline.invoke(PESessionLockingStandardPipeline.java:85)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:185)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:332)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:233)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:165)
at com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:791)
at com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:693)
at com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:954)
at com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:170)
at com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:135)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:102)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:88)
at com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:76)
at com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:53)
at com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:57)
at com.sun.grizzly.ContextTask.run(ContextTask.java:69)
at com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:330)
at com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:309)
at java.lang.Thread.run(Thread.java:662)
|#]
[#|2014-08-05T16:15:29.109+0200|WARNING|glassfishv3.0|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=24;_ThreadName=Thread-1;|StandardWrapperValve[default]: PWC1406: Servlet.service() for servlet default threw exception
java.lang.ClassNotFoundException: com.sun.identity.agents.filter.AmAgentFilter
at org.glassfish.web.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:1985)
at org.glassfish.web.loader.WebappClassLoader.findClass(WebappClassLoader.java:888)
at org.glassfish.web.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1420)
at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:245)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:237)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:277)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:188)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:641)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:97)
at com.sun.enterprise.web.PESessionLockingStandardPipeline.invoke(PESessionLockingStandardPipeline.java:85)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:185)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:332)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:233)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:165)
at com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:791)
at com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:693)
at com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:954)
at com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:170)
at com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:135)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:102)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:88)
at com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:76)
at com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:53)
at com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:57)
at com.sun.grizzly.ContextTask.run(ContextTask.java:69)
at com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:330)
at com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:309)
at java.lang.Thread.run(Thread.java:662)
|#]
Thanks for your time and tips.