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From Ufuk Celebi <...@apache.org>
Subject Re: Integrate Flink with S3 on EMR cluster
Date Tue, 05 Apr 2016 09:18:05 GMT
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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