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From Timur Fayruzov <timur.fairu...@gmail.com>
Subject Re: Integrate Flink with S3 on EMR cluster
Date Tue, 05 Apr 2016 15:47:36 GMT
Hello Ufuk,

I'm using EMR 4.4.0.

Thanks,
Timur

On Tue, Apr 5, 2016 at 2:18 AM, Ufuk Celebi <uce@apache.org> wrote:

> Hey Timur,
>
> which EMR version are you using?
>
> – Ufuk
>
> On Tue, Apr 5, 2016 at 1:43 AM, Timur Fayruzov <timur.fairuzov@gmail.com>
> wrote:
> > Thanks for the answer, Ken.
> >
> > My understanding is that file system selection is driven by the following
> > sections in core-site.xml:
> > <property>
> >   <name>fs.s3.impl</name>
> >   <!--<value>com.amazon.ws.emr.hadoop.fs.EmrFileSystem</value>-->
<!--
> This
> > was the original value -->
> >   <value>org.apache.hadoop.fs.s3native.NativeS3FileSystem</value>
> > </property>
> >
> > <property>
> >   <name>fs.s3n.impl</name>
> >   <value>com.amazon.ws.emr.hadoop.fs.EmrFileSystem</value>
> > </property>
> >
> > If I run the program using configuration above with s3n (and also
> modifying
> > credential keys to use s3n) it fails with the same error, but there is no
> > "... opening key ..." logs. S3a seems to be not supported, it fails with
> the
> > following:
> > Caused by: java.io.IOException: No file system found with scheme s3a,
> > referenced in file URI 's3a://<my key>'.
> > at org.apache.flink.core.fs.FileSystem.get(FileSystem.java:296)
> > at org.apache.flink.core.fs.Path.getFileSystem(Path.java:311)
> > at
> >
> org.apache.flink.api.common.io.FileInputFormat.createInputSplits(FileInputFormat.java:450)
> > at
> >
> org.apache.flink.api.common.io.FileInputFormat.createInputSplits(FileInputFormat.java:57)
> > at
> >
> org.apache.flink.runtime.executiongraph.ExecutionJobVertex.<init>(ExecutionJobVertex.java:156)
> > ... 23 more
> >
> > I am puzzled by the fact that EMRFS is still apparently referenced
> somewhere
> > as an implementation for S3 protocol, I'm not able to locate where this
> > configuration is set.
> >
> >
> > On Mon, Apr 4, 2016 at 4:07 PM, Ken Krugler <kkrugler_lists@transpac.com
> >
> > wrote:
> >>
> >> Normally in Hadoop jobs you’d want to use s3n:// as the protocol, not
> s3.
> >>
> >> Though EMR has some support for magically treating the s3 protocol as
> s3n
> >> (or maybe s3a now, with Hadoop 2.6 or later)
> >>
> >> What happens if you use s3n://<key info>/<path to file> for the
--input
> >> parameter?
> >>
> >> — Ken
> >>
> >> On Apr 4, 2016, at 2:51pm, Timur Fayruzov <timur.fairuzov@gmail.com>
> >> wrote:
> >>
> >> Hello,
> >>
> >> I'm trying to run a Flink WordCount job on an AWS EMR cluster. I
> succeeded
> >> with a three-step procedure: load data from S3 to cluster's HDFS, run
> Flink
> >> Job, unload outputs from HDFS to S3.
> >>
> >> However, ideally I'd like to read/write data directly from/to S3. I
> >> followed the instructions here:
> >>
> https://ci.apache.org/projects/flink/flink-docs-release-1.0/apis/batch/connectors.html
> ,
> >> more specifically I:
> >>   1. Modified flink-conf to point to /etc/hadoop/conf
> >>   2. Modified core-site.xml per link above (not clear why why it is not
> >> using IAM, I had to provide AWS keys explicitly).
> >>
> >> Run the following command:
> >> HADOOP_CONF_DIR=/etc/hadoop/conf flink-1.0.0/bin/flink run -m
> yarn-cluster
> >> -yn 1 -yjm 768 -ytm 768 flink-1.0.0/examples/batch/WordCount.jar --input
> >> s3://<my key> --output hdfs:///flink-output
> >>
> >> First, I see messages like that:
> >> 2016-04-04 21:37:10,418 INFO
> >> org.apache.hadoop.fs.s3native.NativeS3FileSystem              - Opening
> key
> >> '<my key>' for reading at position '333000'
> >>
> >> Then, it fails with the following error:
> >>
> >> ------------------------------------------------------------
> >>
> >>  The program finished with the following exception:
> >>
> >>
> >> org.apache.flink.client.program.ProgramInvocationException: The program
> >> execution failed: Failed to submit job fc13373d993539e647f164e12d82bf90
> >> (WordCount Example)
> >>
> >> at org.apache.flink.client.program.Client.runBlocking(Client.java:381)
> >>
> >> at org.apache.flink.client.program.Client.runBlocking(Client.java:355)
> >>
> >> at org.apache.flink.client.program.Client.runBlocking(Client.java:315)
> >>
> >> at
> >>
> org.apache.flink.client.program.ContextEnvironment.execute(ContextEnvironment.java:60)
> >>
> >> at
> >>
> org.apache.flink.examples.java.wordcount.WordCount.main(WordCount.java:90)
> >>
> >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >>
> >> at
> >>
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> >>
> >> at
> >>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> >>
> >> at java.lang.reflect.Method.invoke(Method.java:606)
> >>
> >> at
> >>
> org.apache.flink.client.program.PackagedProgram.callMainMethod(PackagedProgram.java:505)
> >>
> >> at
> >>
> org.apache.flink.client.program.PackagedProgram.invokeInteractiveModeForExecution(PackagedProgram.java:403)
> >>
> >> at org.apache.flink.client.program.Client.runBlocking(Client.java:248)
> >>
> >> at
> >>
> org.apache.flink.client.CliFrontend.executeProgramBlocking(CliFrontend.java:866)
> >>
> >> at org.apache.flink.client.CliFrontend.run(CliFrontend.java:333)
> >>
> >> at
> >>
> org.apache.flink.client.CliFrontend.parseParameters(CliFrontend.java:1189)
> >>
> >> at org.apache.flink.client.CliFrontend.main(CliFrontend.java:1239)
> >>
> >> Caused by: org.apache.flink.runtime.client.JobExecutionException: Failed
> >> to submit job fc13373d993539e647f164e12d82bf90 (WordCount Example)
> >>
> >> at
> >> org.apache.flink.runtime.jobmanager.JobManager.org
> $apache$flink$runtime$jobmanager$JobManager$$submitJob(JobManager.scala:1100)
> >>
> >> at
> >>
> org.apache.flink.runtime.jobmanager.JobManager$$anonfun$handleMessage$1.applyOrElse(JobManager.scala:380)
> >>
> >> at
> >>
> scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
> >>
> >> at
> >>
> org.apache.flink.yarn.YarnJobManager$$anonfun$handleYarnMessage$1.applyOrElse(YarnJobManager.scala:153)
> >>
> >> at scala.PartialFunction$OrElse.apply(PartialFunction.scala:167)
> >>
> >> at
> >>
> org.apache.flink.runtime.LeaderSessionMessageFilter$$anonfun$receive$1.applyOrElse(LeaderSessionMessageFilter.scala:36)
> >>
> >> at
> >>
> scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
> >>
> >> at
> >> org.apache.flink.runtime.LogMessages$$anon$1.apply(LogMessages.scala:33)
> >>
> >> at
> >> org.apache.flink.runtime.LogMessages$$anon$1.apply(LogMessages.scala:28)
> >>
> >> at scala.PartialFunction$class.applyOrElse(PartialFunction.scala:123)
> >>
> >> at
> >>
> org.apache.flink.runtime.LogMessages$$anon$1.applyOrElse(LogMessages.scala:28)
> >>
> >> at akka.actor.Actor$class.aroundReceive(Actor.scala:465)
> >>
> >> at
> >>
> org.apache.flink.runtime.jobmanager.JobManager.aroundReceive(JobManager.scala:106)
> >>
> >> at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
> >>
> >> at akka.actor.ActorCell.invoke(ActorCell.scala:487)
> >>
> >> at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:254)
> >>
> >> at akka.dispatch.Mailbox.run(Mailbox.scala:221)
> >>
> >> at akka.dispatch.Mailbox.exec(Mailbox.scala:231)
> >>
> >> at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
> >>
> >> at
> >>
> scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
> >>
> >> at
> >> scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
> >>
> >> at
> >>
> scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
> >>
> >> Caused by: org.apache.flink.runtime.JobException: Creating the input
> >> splits caused an error:
> >>
> org.apache.hadoop.conf.Configuration.addResource(Lorg/apache/hadoop/conf/Configuration;)V
> >>
> >> at
> >>
> org.apache.flink.runtime.executiongraph.ExecutionJobVertex.<init>(ExecutionJobVertex.java:172)
> >>
> >> at
> >>
> org.apache.flink.runtime.executiongraph.ExecutionGraph.attachJobGraph(ExecutionGraph.java:696)
> >>
> >> at
> >> org.apache.flink.runtime.jobmanager.JobManager.org
> $apache$flink$runtime$jobmanager$JobManager$$submitJob(JobManager.scala:1023)
> >>
> >> ... 21 more
> >>
> >> Caused by: java.lang.NoSuchMethodError:
> >>
> org.apache.hadoop.conf.Configuration.addResource(Lorg/apache/hadoop/conf/Configuration;)V
> >>
> >> at
> >>
> com.amazon.ws.emr.hadoop.fs.EmrFileSystem.initialize(EmrFileSystem.java:96)
> >>
> >> at
> >>
> org.apache.flink.runtime.fs.hdfs.HadoopFileSystem.initialize(HadoopFileSystem.java:321)
> >>
> >> at org.apache.flink.core.fs.FileSystem.get(FileSystem.java:291)
> >>
> >> at org.apache.flink.core.fs.Path.getFileSystem(Path.java:311)
> >>
> >> at
> >>
> org.apache.flink.api.common.io.FileInputFormat.createInputSplits(FileInputFormat.java:450)
> >>
> >> at
> >>
> org.apache.flink.api.common.io.FileInputFormat.createInputSplits(FileInputFormat.java:57)
> >>
> >> at
> >>
> org.apache.flink.runtime.executiongraph.ExecutionJobVertex.<init>(ExecutionJobVertex.java:156)
> >>
> >> ... 23 more
> >>
> >>
> >> Somehow, it's still tries to use EMRFS (which may be a valid thing?),
> but
> >> it is failing to initialize. I don't know enough about EMRFS/S3 interop
> so
> >> don't know how diagnose it further.
> >>
> >> I run Flink 1.0.0 compiled for Scala 2.11.
> >>
> >> Any advice on how to make it work is highly appreciated.
> >>
> >>
> >> Thanks,
> >>
> >> Timur
> >>
> >>
> >>
> >>
> >> --------------------------
> >> Ken Krugler
> >> +1 530-210-6378
> >> http://www.scaleunlimited.com
> >> custom big data solutions & training
> >> Hadoop, Cascading, Cassandra & Solr
> >>
> >>
> >>
> >>
> >>
> >
>

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