Strange spark ERROR on AWS EMR

24
votes

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

2
amazon-web-servicesapache-sparkpysparkamazon-emr
Are you creating multiple SparkContexts by any chance ? - Alex
No I have only one SparkContext. - seiya
I just ran into this after upgrading to emr 5.10.0. Running exactly the same code on 5.9.0 did not throw the error. In my case I'm using scala and actually calling .get on an option, so the error makes more sense, but I'm always calling it in a safe manner and should never get this error. Plus, my code still seems to work just fine. - Tim Gautier
I am also getting this error when running the EMR cluster in a VPC with a VPN connection to our corporate data center. When I run the same code on an EMR cluster with the default VPC, the error does not appear. I suspect some DNS configuration issues. - Marius Ion
@Traveler I am still seeing this error with EMR 5.11.0 - seiya

2 Answers

18
votes

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 :)

6
votes

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.