spark-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Koert Kuipers <ko...@tresata.com>
Subject Re: spark 0.8
Date Fri, 18 Oct 2013 16:49:30 GMT
at this point i feel like it must be some sort of version mismatch? i am
gonna check the spark build that i deployed on the cluster


On Fri, Oct 18, 2013 at 12:46 PM, Koert Kuipers <koert@tresata.com> wrote:

> name := "Simple Project"
>
> version := "1.0"
>
> scalaVersion := "2.9.3"
>
> libraryDependencies += "org.apache.spark" %% "spark-core" %
> "0.8.0-incubating"
>
> resolvers += "Akka Repository" at "http://repo.akka.io/releases/"
>
> resolvers += "Cloudera Repository" at "
> https://repository.cloudera.com/artifactory/cloudera-repos/"
>
> libraryDependencies += "org.apache.hadoop" % "hadoop-client" %
> "2.0.0-mr1-cdh4.3.0"
>
>
>
>
> On Fri, Oct 18, 2013 at 12:34 PM, Matei Zaharia <matei.zaharia@gmail.com>wrote:
>
>> Can you post the build.sbt for your program? It needs to include
>> hadoop-client for CDH4.3, and that should *not* be listed as provided.
>>
>> Matei
>>
>> On Oct 18, 2013, at 8:23 AM, Koert Kuipers <koert@tresata.com> wrote:
>>
>> ok this has nothing to do with hadoop access. even a simple program that
>> uses sc.parallelize blows up in this way.
>>
>> so spark-shell works well on the same machine i launch this from.
>>
>> if i launch a simple program without using kryo for serializer and
>> closure serialize i get a different error. see below.
>> at this point it seems to me i have some issue with task serialization???
>>
>>
>>
>> 13/10/18 11:20:37 INFO StandaloneExecutorBackend: Got assigned task 0
>> 13/10/18 11:20:37 INFO StandaloneExecutorBackend: Got assigned task 1
>> 13/10/18 11:20:37 INFO Executor: Running task ID 1
>> 13/10/18 11:20:37 INFO Executor: Running task ID 0
>> 13/10/18 11:20:37 INFO Executor: Fetching
>> http://192.168.3.171:41629/jars/simple-project_2.9.3-1.0.jar with
>> timestamp 1382109635095
>> 13/10/18 11:20:37 INFO Utils: Fetching
>> http://192.168.3.171:41629/jars/simple-project_2.9.3-1.0.jar to
>> /tmp/fetchFileTemp378181753997570700.tmp
>> 13/10/18 11:20:37 INFO Executor: Adding
>> file:/var/lib/spark/app-20131018112035-0014/1/./simple-project_2.9.3-1.0.jar
>> to class loader
>> 13/10/18 11:20:37 INFO Executor: caught throwable with stacktrace
>> java.io.StreamCorruptedException: invalid type code: 00
>>     at
>> java.io.ObjectInputStream$BlockDataInputStream.readBlockHeader(ObjectInputStream.java:2467)
>>     at
>> java.io.ObjectInputStream$BlockDataInputStream.refill(ObjectInputStream.java:2502)
>>     at
>> java.io.ObjectInputStream$BlockDataInputStream.read(ObjectInputStream.java:2661)
>>     at
>> java.io.ObjectInputStream$BlockDataInputStream.read(ObjectInputStream.java:2583)
>>     at java.io.DataInputStream.readFully(DataInputStream.java:178)
>>     at java.io.DataInputStream.readLong(DataInputStream.java:399)
>>     at
>> java.io.ObjectInputStream$BlockDataInputStream.readLong(ObjectInputStream.java:2803)
>>     at java.io.ObjectInputStream.readLong(ObjectInputStream.java:958)
>>     at
>> org.apache.spark.rdd.ParallelCollectionPartition.readObject(ParallelCollectionRDD.scala:72)
>>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>     at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>     at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>     at java.lang.reflect.Method.invoke(Method.java:597)
>>     at
>> java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:969)
>>     at
>> java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1852)
>>     at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1756)
>>     at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1326)
>>     at java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)
>>     at
>> org.apache.spark.scheduler.ResultTask.readExternal(ResultTask.scala:135)
>>     at
>> java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1795)
>>     at
>> java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1754)
>>     at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1326)
>>     at java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)
>>     at
>> org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:39)
>>     at
>> org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:61)
>>     at
>> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:153)
>>     at
>> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
>>     at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
>>     at java.lang.Thread.run(Thread.java:662)
>>
>>
>>
>> On Fri, Oct 18, 2013 at 10:59 AM, Koert Kuipers <koert@tresata.com>wrote:
>>
>>> i created a tiny sbt project as described here:
>>> apache.org/docs/latest/quick-start.html#a-standalone-app-in-scala<http://spark.incubator.apache.org/docs/latest/quick-start.html#a-standalone-app-in-scala>
>>>
>>> it has the correct dependencies: spark-core and the correct
>>> hadoop-client for my platform. i tried both the generic spark-core
>>> dependency and spark-core dependency compiled against my platform. it runs
>>> fine in local mode, but when i switch to the cluster i still always get the
>>> following exceptions on tasks:
>>>
>>> 13/10/18 10:25:53 ERROR Executor: Uncaught exception in thread
>>> Thread[pool-5-thread-1,5,main]
>>>
>>> java.lang.NullPointerException
>>>     at
>>> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:187)
>>>     at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
>>>     at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
>>>     at java.lang.Thread.run(Thread.java:662)
>>>
>>> after adding some additional debugging to Executor i see the cause is
>>> this:
>>> 13/10/18 10:54:47 INFO Executor: caught throwable with stacktrace
>>> java.lang.NullPointerException
>>>     at
>>> org.apache.spark.executor.Executor$TaskRunner$$anonfun$run$2.apply(Executor.scala:155)
>>>     at
>>> org.apache.spark.executor.Executor$TaskRunner$$anonfun$run$2.apply(Executor.scala:155)
>>>     at org.apache.spark.Logging$class.logInfo(Logging.scala:48)
>>>     at org.apache.spark.executor.Executor.logInfo(Executor.scala:36)
>>>     at
>>> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:155)
>>>
>>>     at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
>>>     at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
>>>     at java.lang.Thread.run(Thread.java:662)
>>>
>>> so it seems the offending line is:
>>> logInfo("Its epoch is " + task.epoch)
>>>
>>> i am guessing accessing epoch on the task is throwing the NPE. any ideas?
>>>
>>>
>>>
>>> On Thu, Oct 17, 2013 at 8:12 PM, Koert Kuipers <koert@tresata.com>wrote:
>>>
>>>> sorry one more related question:
>>>> i compile against a spark build for hadoop 1.0.4, but the actual
>>>> installed version of spark is build against cdh4.3.0-mr1. this also used
to
>>>> work, and i prefer to do this so i compile against a generic spark build.
>>>> could this be the issue?
>>>>
>>>>
>>>> On Thu, Oct 17, 2013 at 8:06 PM, Koert Kuipers <koert@tresata.com>wrote:
>>>>
>>>>> i have my spark and hadoop related dependencies as "provided" for my
>>>>> spark job. this used to work with previous versions. are these now supposed
>>>>> to be compile/runtime/default dependencies?
>>>>>
>>>>>
>>>>> On Thu, Oct 17, 2013 at 8:04 PM, Koert Kuipers <koert@tresata.com>wrote:
>>>>>
>>>>>> yes i did that and i can see the correct jars sitting in lib_managed
>>>>>>
>>>>>>
>>>>>> On Thu, Oct 17, 2013 at 7:56 PM, Matei Zaharia <
>>>>>> matei.zaharia@gmail.com> wrote:
>>>>>>
>>>>>>> Koert, did you link your Spark job to the right version of HDFS
as
>>>>>>> well? In Spark 0.8, you have to add a Maven dependency on "hadoop-client"
>>>>>>> for your version of Hadoop. See
>>>>>>> http://spark.incubator.apache.org/docs/latest/quick-start.html#a-standalone-app-in-scala
for
>>>>>>> example.
>>>>>>>
>>>>>>> Matei
>>>>>>>
>>>>>>> On Oct 17, 2013, at 4:38 PM, Koert Kuipers <koert@tresata.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>> i got the job a little further along by also setting this:
>>>>>>> System.setProperty("spark.closure.serializer",
>>>>>>> "org.apache.spark.serializer.KryoSerializer")
>>>>>>>
>>>>>>> not sure why i need to... but anyhow, now my workers start and
then
>>>>>>> they blow up on this:
>>>>>>>
>>>>>>> 13/10/17 19:22:57 ERROR Executor: Uncaught exception in thread
>>>>>>> Thread[pool-5-thread-1,5,main]
>>>>>>> java.lang.NullPointerException
>>>>>>>     at
>>>>>>> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:187)
>>>>>>>     at
>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
>>>>>>>     at
>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
>>>>>>>     at java.lang.Thread.run(Thread.java:662)
>>>>>>>
>>>>>>>
>>>>>>> which is:
>>>>>>>  val metrics = attemptedTask.flatMap(t => t.metrics)
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Oct 17, 2013 at 7:30 PM, dachuan <hdc1112@gmail.com>
wrote:
>>>>>>>
>>>>>>>> thanks, Mark.
>>>>>>>>
>>>>>>>>
>>>>>>>> On Thu, Oct 17, 2013 at 6:36 PM, Mark Hamstra <
>>>>>>>> mark@clearstorydata.com> wrote:
>>>>>>>>
>>>>>>>>> SNAPSHOTs are not fixed versions, but are floating names
>>>>>>>>> associated with whatever is the most recent code.  So,
Spark 0.8.0 is the
>>>>>>>>> current released version of Spark, which is exactly the
same today as it
>>>>>>>>> was yesterday, and will be the same thing forever.  Spark
0.8.1-SNAPSHOT is
>>>>>>>>> whatever is currently in branch-0.8.  It changes every
time new code is
>>>>>>>>> committed to that branch (which should be just bug fixes
and the few
>>>>>>>>> additional features that we wanted to get into 0.8.0,
but that didn't quite
>>>>>>>>> make it.)  Not too long from now there will be a release
of Spark 0.8.1, at
>>>>>>>>> which time the SNAPSHOT will got to 0.8.2 and 0.8.1 will
be forever frozen.
>>>>>>>>>  Meanwhile, the wild new development is taking place
on the master branch,
>>>>>>>>> and whatever is currently in that branch becomes 0.9.0-SNAPSHOT.
 This
>>>>>>>>> could be quite different from day to day, and there are
no guarantees that
>>>>>>>>> things won't be broken in 0.9.0-SNAPSHOT.  Several months
from now there
>>>>>>>>> will be a release of Spark 0.9.0 (unless the decision
is made to bump the
>>>>>>>>> version to 1.0.0), at which point the SNAPSHOT goes to
0.9.1 and the whole
>>>>>>>>> process advances to the next phase of development.
>>>>>>>>>
>>>>>>>>> The short answer is that releases are stable, SNAPSHOTs
are not,
>>>>>>>>> and SNAPSHOTs that aren't on maintenance branches can
break things.  You
>>>>>>>>> make your choice of which to use and pay the consequences.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, Oct 17, 2013 at 3:18 PM, dachuan <hdc1112@gmail.com>wrote:
>>>>>>>>>
>>>>>>>>>> yeah, I mean 0.9.0-SNAPSHOT. I use git clone and
that's what I
>>>>>>>>>> got.. what's the difference? I mean SNAPSHOT and
non-SNAPSHOT.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Thu, Oct 17, 2013 at 6:15 PM, Mark Hamstra <
>>>>>>>>>> mark@clearstorydata.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Of course, you mean 0.9.0-SNAPSHOT.  There is
no Spark 0.9.0,
>>>>>>>>>>> and won't be for several months.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Thu, Oct 17, 2013 at 3:11 PM, dachuan <hdc1112@gmail.com>wrote:
>>>>>>>>>>>
>>>>>>>>>>>> I'm sorry if this doesn't answer your question
directly, but I
>>>>>>>>>>>> have tried spark 0.9.0 and hdfs 1.0.4 just
now, it works..
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Thu, Oct 17, 2013 at 6:05 PM, Koert Kuipers
<
>>>>>>>>>>>> koert@tresata.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> after upgrading from spark 0.7 to spark
0.8 i can no longer
>>>>>>>>>>>>> access any files on HDFS.
>>>>>>>>>>>>>  i see the error below. any ideas?
>>>>>>>>>>>>>
>>>>>>>>>>>>> i am running spark standalone on a cluster
that also has
>>>>>>>>>>>>> CDH4.3.0 and rebuild spark accordingly.
the jars in lib_managed look good
>>>>>>>>>>>>> to me.
>>>>>>>>>>>>>
>>>>>>>>>>>>> i noticed similar errors in the mailing
list but found no
>>>>>>>>>>>>> suggested solutions.
>>>>>>>>>>>>>
>>>>>>>>>>>>> thanks! koert
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> 13/10/17 17:43:23 ERROR Executor: Exception
in task ID 0
>>>>>>>>>>>>> java.io.EOFException
>>>>>>>>>>>>> 	at java.io.ObjectInputStream$BlockDataInputStream.readFully(ObjectInputStream.java:2703)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readFully(ObjectInputStream.java:1008)
>>>>>>>>>>>>> 	at org.apache.hadoop.io.DataOutputBuffer$Buffer.write(DataOutputBuffer.java:68)
>>>>>>>>>>>>> 	at org.apache.hadoop.io.DataOutputBuffer.write(DataOutputBuffer.java:106)
>>>>>>>>>>>>> 	at org.apache.hadoop.io.UTF8.readChars(UTF8.java:258)
>>>>>>>>>>>>> 	at org.apache.hadoop.io.UTF8.readString(UTF8.java:250)
>>>>>>>>>>>>> 	at org.apache.hadoop.mapred.FileSplit.readFields(FileSplit.java:87)
>>>>>>>>>>>>> 	at org.apache.hadoop.io.ObjectWritable.readObject(ObjectWritable.java:280)
>>>>>>>>>>>>> 	at org.apache.hadoop.io.ObjectWritable.readFields(ObjectWritable.java:75)
>>>>>>>>>>>>> 	at org.apache.spark.SerializableWritable.readObject(SerializableWritable.scala:39)
>>>>>>>>>>>>> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
>>>>>>>>>>>>> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>>>>>>>>>>> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>>>>>>>>>>> 	at java.lang.reflect.Method.invoke(Method.java:597)
>>>>>>>>>>>>> 	at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:969)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1852)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1756)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1326)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1950)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1874)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1756)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1326)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)
>>>>>>>>>>>>> 	at org.apache.spark.scheduler.ResultTask.readExternal(ResultTask.scala:135)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1795)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1754)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1326)
>>>>>>>>>>>>> 	at java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)
>>>>>>>>>>>>> 	at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:39)
>>>>>>>>>>>>> 	at org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:61)
>>>>>>>>>>>>> 	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:153)
>>>>>>>>>>>>> 	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
>>>>>>>>>>>>> 	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
>>>>>>>>>>>>> 	at java.lang.Thread.run(Thread.java:662)
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Dachuan Huang
>>>>>>>>>>>> Cellphone: 614-390-7234
>>>>>>>>>>>> 2015 Neil Avenue
>>>>>>>>>>>> Ohio State University
>>>>>>>>>>>> Columbus, Ohio
>>>>>>>>>>>> U.S.A.
>>>>>>>>>>>> 43210
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Dachuan Huang
>>>>>>>>>> Cellphone: 614-390-7234
>>>>>>>>>> 2015 Neil Avenue
>>>>>>>>>> Ohio State University
>>>>>>>>>> Columbus, Ohio
>>>>>>>>>> U.S.A.
>>>>>>>>>> 43210
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Dachuan Huang
>>>>>>>> Cellphone: 614-390-7234
>>>>>>>> 2015 Neil Avenue
>>>>>>>> Ohio State University
>>>>>>>> Columbus, Ohio
>>>>>>>> U.S.A.
>>>>>>>> 43210
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>

Mime
View raw message