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From Patrick Wendell <pwend...@gmail.com>
Subject Re: ec2 clusters launched at 9fe693b5b6 are broken (?)
Date Tue, 15 Jul 2014 05:19:17 GMT
Yeah - this is likely caused by SPARK-2471.

On Mon, Jul 14, 2014 at 10:11 PM, Shivaram Venkataraman
<shivaram@eecs.berkeley.edu> wrote:
> My guess is that this is related to
> https://issues.apache.org/jira/browse/SPARK-2471 where the S3 library gets
> excluded from the SBT assembly jar. I am not sure if the assembly jar used
> in EC2 is generated using SBT though.
>
> Shivaram
>
>
> On Mon, Jul 14, 2014 at 10:02 PM, Aaron Davidson <ilikerps@gmail.com> wrote:
>
>> This one is typically due to a mismatch between the Hadoop versions --
>> i.e., Spark is compiled against 1.0.4 but is running with 2.3.0 in the
>> classpath, or something like that. Not certain why you're seeing this with
>> spark-ec2, but I'm assuming this is related to the issues you posted in a
>> separate thread.
>>
>>
>> On Mon, Jul 14, 2014 at 6:43 PM, Nicholas Chammas <
>> nicholas.chammas@gmail.com> wrote:
>>
>> > Just launched an EC2 cluster from git hash
>> > 9fe693b5b6ed6af34ee1e800ab89c8a11991ea38. Calling take() on an RDD
>> > accessing data in S3 yields the following error output.
>> >
>> > I understand that NoClassDefFoundError errors may mean something in the
>> > deployment was messed up. Is that correct? When I launch a cluster using
>> > spark-ec2, I expect all critical deployment details to be taken care of
>> by
>> > the script.
>> >
>> > So is something in the deployment executed by spark-ec2 borked?
>> >
>> > Nick
>> >
>> > java.lang.NoClassDefFoundError: org/jets3t/service/S3ServiceException
>> >     at
>> >
>> org.apache.hadoop.fs.s3native.NativeS3FileSystem.createDefaultStore(NativeS3FileSystem.java:224)
>> >     at
>> >
>> org.apache.hadoop.fs.s3native.NativeS3FileSystem.initialize(NativeS3FileSystem.java:214)
>> >     at
>> > org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:1386)
>> >     at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:66)
>> >     at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:1404)
>> >     at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:254)
>> >     at org.apache.hadoop.fs.Path.getFileSystem(Path.java:187)
>> >     at
>> >
>> org.apache.hadoop.mapred.FileInputFormat.listStatus(FileInputFormat.java:176)
>> >     at
>> >
>> org.apache.hadoop.mapred.FileInputFormat.getSplits(FileInputFormat.java:208)
>> >     at org.apache.spark.rdd.HadoopRDD.getPartitions(HadoopRDD.scala:176)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:203)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
>> >     at scala.Option.getOrElse(Option.scala:120)
>> >     at org.apache.spark.rdd.RDD.partitions(RDD.scala:201)
>> >     at org.apache.spark.rdd.MappedRDD.getPartitions(MappedRDD.scala:28)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:203)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
>> >     at scala.Option.getOrElse(Option.scala:120)
>> >     at org.apache.spark.rdd.RDD.partitions(RDD.scala:201)
>> >     at
>> >
>> org.apache.spark.rdd.MapPartitionsRDD.getPartitions(MapPartitionsRDD.scala:32)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:203)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
>> >     at scala.Option.getOrElse(Option.scala:120)
>> >     at org.apache.spark.rdd.RDD.partitions(RDD.scala:201)
>> >     at org.apache.spark.ShuffleDependency.<init>(Dependency.scala:71)
>> >     at
>> > org.apache.spark.rdd.ShuffledRDD.getDependencies(ShuffledRDD.scala:79)
>> >     at
>> > org.apache.spark.rdd.RDD$$anonfun$dependencies$2.apply(RDD.scala:190)
>> >     at
>> > org.apache.spark.rdd.RDD$$anonfun$dependencies$2.apply(RDD.scala:188)
>> >     at scala.Option.getOrElse(Option.scala:120)
>> >     at org.apache.spark.rdd.RDD.dependencies(RDD.scala:188)
>> >     at
>> >
>> org.apache.spark.scheduler.DAGScheduler.getPreferredLocs(DAGScheduler.scala:1144)
>> >     at
>> > org.apache.spark.SparkContext.getPreferredLocs(SparkContext.scala:903)
>> >     at
>> >
>> org.apache.spark.rdd.PartitionCoalescer.currPrefLocs(CoalescedRDD.scala:174)
>> >     at
>> >
>> org.apache.spark.rdd.PartitionCoalescer$LocationIterator$$anonfun$4$$anonfun$apply$2.apply(CoalescedRDD.scala:191)
>> >     at
>> >
>> org.apache.spark.rdd.PartitionCoalescer$LocationIterator$$anonfun$4$$anonfun$apply$2.apply(CoalescedRDD.scala:190)
>> >     at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
>> >     at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
>> >     at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:350)
>> >     at
>> >
>> org.apache.spark.rdd.PartitionCoalescer$LocationIterator.<init>(CoalescedRDD.scala:185)
>> >     at
>> >
>> org.apache.spark.rdd.PartitionCoalescer.setupGroups(CoalescedRDD.scala:236)
>> >     at
>> org.apache.spark.rdd.PartitionCoalescer.run(CoalescedRDD.scala:337)
>> >     at
>> > org.apache.spark.rdd.CoalescedRDD.getPartitions(CoalescedRDD.scala:83)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:203)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
>> >     at scala.Option.getOrElse(Option.scala:120)
>> >     at org.apache.spark.rdd.RDD.partitions(RDD.scala:201)
>> >     at org.apache.spark.rdd.MappedRDD.getPartitions(MappedRDD.scala:28)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:203)
>> >     at
>> org.apache.spark.rdd.RDD$$anonfun$partitions$2.apply(RDD.scala:201)
>> >     at scala.Option.getOrElse(Option.scala:120)
>> >     at org.apache.spark.rdd.RDD.partitions(RDD.scala:201)
>> >     at org.apache.spark.rdd.RDD.take(RDD.scala:1036)
>> >     at $iwC$$iwC$$iwC$$iwC.<init>(<console>:26)
>> >     at $iwC$$iwC$$iwC.<init>(<console>:31)
>> >     at $iwC$$iwC.<init>(<console>:33)
>> >     at $iwC.<init>(<console>:35)
>> >     at <init>(<console>:37)
>> >     at .<init>(<console>:41)
>> >     at .<clinit>(<console>)
>> >     at .<init>(<console>:7)
>> >     at .<clinit>(<console>)
>> >     at $print(<console>)
>> >     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> >     at
>> >
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>> >     at
>> >
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> >     at java.lang.reflect.Method.invoke(Method.java:606)
>> >     at
>> > org.apache.spark.repl.SparkIMain$ReadEvalPrint.call(SparkIMain.scala:788)
>> >     at
>> >
>> org.apache.spark.repl.SparkIMain$Request.loadAndRun(SparkIMain.scala:1056)
>> >     at
>> > org.apache.spark.repl.SparkIMain.loadAndRunReq$1(SparkIMain.scala:614)
>> >     at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:645)
>> >     at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:609)
>> >     at
>> > org.apache.spark.repl.SparkILoop.reallyInterpret$1(SparkILoop.scala:796)
>> >     at
>> >
>> org.apache.spark.repl.SparkILoop.interpretStartingWith(SparkILoop.scala:841)
>> >     at org.apache.spark.repl.SparkILoop.command(SparkILoop.scala:753)
>> >     at
>> org.apache.spark.repl.SparkILoop.processLine$1(SparkILoop.scala:601)
>> >     at org.apache.spark.repl.SparkILoop.innerLoop$1(SparkILoop.scala:608)
>> >     at org.apache.spark.repl.SparkILoop.loop(SparkILoop.scala:611)
>> >     at
>> >
>> org.apache.spark.repl.SparkILoop$$anonfun$process$1.apply$mcZ$sp(SparkILoop.scala:936)
>> >     at
>> >
>> org.apache.spark.repl.SparkILoop$$anonfun$process$1.apply(SparkILoop.scala:884)
>> >     at
>> >
>> org.apache.spark.repl.SparkILoop$$anonfun$process$1.apply(SparkILoop.scala:884)
>> >     at
>> >
>> scala.tools.nsc.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:135)
>> >     at org.apache.spark.repl.SparkILoop.process(SparkILoop.scala:884)
>> >     at org.apache.spark.repl.SparkILoop.process(SparkILoop.scala:982)
>> >     at org.apache.spark.repl.Main$.main(Main.scala:31)
>> >     at org.apache.spark.repl.Main.main(Main.scala)
>> >     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> >     at
>> >
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>> >     at
>> >
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> >     at java.lang.reflect.Method.invoke(Method.java:606)
>> >     at org.apache.spark.deploy.SparkSubmit$.launch(SparkSubmit.scala:303)
>> >     at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:55)
>> >     at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
>> > Caused by: java.lang.ClassNotFoundException:
>> > org.jets3t.service.S3ServiceException
>> >     at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>> >     at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>> >     at java.security.AccessController.doPrivileged(Native Method)
>> >     at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>> >     at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
>> >     at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
>> >     at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
>> >     ... 92 more
>> >
>> >
>> >
>>

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