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From Rohit Bhat <rohitbhat.n...@gmail.com>
Subject Re: Issue while executing SimpleShortestPathsComputation
Date Mon, 09 Dec 2013 18:34:24 GMT
Hi Alexandre,

I looked into the logs and found this:

2013-12-09 12:29:08,925 INFO  [main] yarn.GiraphApplicationMaster
(GiraphApplicationMaster.java:main(426)) - Starting GitaphAM
2013-12-09 12:29:09,727 WARN  [main] util.NativeCodeLoader
(NativeCodeLoader.java:<clinit>(62)) - Unable to load native-hadoop library
for your$
2013-12-09 12:29:10,206 ERROR [main] yarn.GiraphApplicationMaster
(GiraphApplicationMaster.java:main(442)) - GiraphApplicationMaster caught a
t$
java.lang.NoClassDefFoundError: org/apache/hadoop/mapreduce/lib/output/
*TextOutputFormat*
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:788)
        at
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)

In gam-stderr.log i found this:

SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in
[jar:file:/scratch/rohit/hadoop-2.2.0/tmp/nm-local-dir/usercache/rohit/appcache/application_1386613677359_0001/filecach$
SLF4J: Found binding in
[jar:file:/scratch/rohit/hadoop-2.2.0/share/hadoop/common/lib/slf4j-log4j12-1.7.5.jar!/org/slf4j/impl/StaticLoggerBinde$

I tried the fix that you mentioned of linking and adding -yj for hadoop-
mapreduce-client-core-2.2.0.jar but that did not help. HADOOP_MAPRED_HOME
is pointing to HADOOP_HOME on my setup.


On Mon, Dec 9, 2013 at 10:11 AM, Alexandre Fonseca <
alexandrejorgefonseca@gmail.com> wrote:

> Hi Rohit,
>
> In my case, I got 2 Shell$ExitCodeExceptions when trying to run the
> SimpleShortestPathsComputation:
>
> - Error: Could not find or load main class
> org.apache.giraph.yarn.GiraphApplicationMaster
>
>   This was solved by adding -yj giraph-examples-1.1.0-SNAPSHOT-for-
> hadoop-2.2.0-jar-with-dependencies.jar
>
> - java.lang.NoClassDefFoundError:
> org/apache/hadoop/mapreduce/lib/output/TextOutputFormat
>
>    This was solved by making sure HADOOP_MAPRED_HOME was
> pointing to the same directory as HADOOP_PREFIX or HADOOP_HOME and
> restarting
> both the nodemanager and resourcemanager. Another thing that also worked
> was
> linking the $HADOOP_PREFIX/share/hadoop/mapreduce/hadoop-mapreduce-client-
> core-2.2.0.jar file to the current directory and adding it to the -yj
> parameter:
>         -yj giraph-examples-1.1.0-SNAPSHOT-for-hadoop-2.2.0-jar-with-
> dependencies.jar,hadoop-mapreduce-client-core-2.2.0.jar
>
> I found the first error on:
>
> /home/alex/Programs/hadoop-2.2.0/logs/userlogs/application_1386443083254_0001/container_
> 1386443083254_0001_01_000001/gam-stderr.log
>
> And the second error on:
>
> /home/alex/Programs/hadoop-2.2.0/logs/userlogs/application_1386443083254_0002/container_
> 1386443083254_0001_01_000002/gam-stdout.log
>
> If you didn't change the default yarn property yarn.nodemanager.log-dirs,
> you
> should be able to see them on the respective directories on your side. If
> not,
> check on whatever you set that property to.
>
> Hope this helps!
>
> Alex
>
> On Monday 09 December 2013 09:50:35 Rohit Bhat wrote:
> > Hi Eli/Alexandre,
> >
> > I have tried with Giraph-1.1.0-SNAPSHOT and hadoop-2.2.0 as well using
> the
> > steps mentioned by Alexandre, but again i am getting the same error while
> > running the example:
> >
> > Command:
> >
> > $HADOOP_HOME/bin/hadoop jar
> > giraph-examples-1.1.0-SNAPSHOT-for-hadoop-2.2.0-jar-with-dependencies.jar
> > org.apache.giraph.GiraphRunner
> > org.apache.giraph.examples.SimpleShortestPathsComputation -vif
> > org.apache.giraph.io.formats.JsonLongDoubleFloatDoubleVertexInputFormat
> > -vip /giraphInput/tiny_graph.txt -vof
> > org.apache.giraph.io.formats.IdWithValueTextOutputFormat -op
> > /output/shortestpaths -w 1 -ca giraph.SplitMasterWorker=false -ca
> > giraph.zkList=localhost:2181 -yj
> > giraph-examples-1.1.0-SNAPSHOT-for-hadoop-2.2.0-jar-with-dependencies.jar
> >
> > ERROR yarn.GiraphYarnClient: Giraph:
> > org.apache.giraph.examples.SimpleShortestPathsComputation reports FAILED
> > state, diagnostics show: Application application_1386601013698_0005
> failed
> > 2 times due to AM Container for appattempt_1386601013698_0005_000002
> exited
> > with  exitCode: 1 due to: Exception from container-launch:
> > org.apache.hadoop.util.Shell$ExitCodeException:
> > at org.apache.hadoop.util.Shell.runCommand(Shell.java:464)
> > at org.apache.hadoop.util.Shell.run(Shell.java:379)
> > at
> org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:589)
> > at
> >
> org.apache.hadoop.yarn.server.nodemanager.DefaultContainerExecutor.launchCon
> > tainer(DefaultContainerExecutor.java:195) at
> >
> org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.Containe
> > rLaunch.call(ContainerLaunch.java:283) at
> >
> org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.Containe
> > rLaunch.call(ContainerLaunch.java:79) at
> > java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at
> > java.util.concurrent.FutureTask.run(FutureTask.java:166)
> > at
> >
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:11
> > 45) at
> >
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:6
> > 15) at java.lang.Thread.run(Thread.java:724)
> >
> >
> > .Failing this attempt.. Failing the application.
> >
> > I checked the Hadoop logs as well but couldn't find anything meaningful
> > there too.
> >
> > Thanks,
> > Rohit
> >
> > On Sun, Dec 8, 2013 at 12:02 PM, Eli Reisman
> <apache.mailbox@gmail.com>wrote:
> > > Hey all,
> > >
> > > So. I think from more recent emails Rohit got this figured out, but, a
> > > couple points just so they out there again:
> > >
> > > Giraph 1.0.x can be built on a "pure YARN" profile with Hadoop
> > > 2.0.03-alpha or (with a patch thats still floating around on GIRAPH-687
> > > ticket) against Hadoop 2.0.4 and 2.0.5 alpha.
> > >
> > > Much better way to go is to build against Hadoop 2.2.x line using
> Giraph
> > > 1.1.x's YARN profile. This features a stable API, some basic support
> for
> > > security, and a concurrency fix that could bite you when launching many
> > > workers.
> > >
> > > Finally, you _can_ run Giraph on MRv2 on YARN in which case you need to
> > > build against a Hadoop 2.x Giraph Maven profile but _not_ the YARN
> > > profile.
> > > This runs on top of MapReduce just as Giraph on Hadoop 1.x or 0.20.x
> do,
> > > but riding on Mapper task instead of running the workers in YARN
> > > containers.
> > >
> > >
> > >
> > > On Sat, Dec 7, 2013 at 8:53 PM, Alexandre Fonseca <
> > >
> > > alexandrejorgefonseca@gmail.com> wrote:
> > >> Hello Yong,
> > >>
> > >> I was able to compile and run Giraph 1.1.0-SNAPSHOT on top of
> > >> hadoop-2.2.0.
> > >>
> > >> Here's what I did:
> > >>         git clone https://git-wip-us.apache.org/repos/asf/giraph.git
> > >>         cd giraph
> > >>         git revert ac93c3b6c5bce5f22b293b29df91663ca7d7ce63
> > >>         mvn -Phadoop_yarn -Dhadoop.version=2.2.0 -DskipTests compile
> > >>
> > >> With that I got valid jars which allowed me to run the
> > >> SimpleShortestPaths
> > >>
> > >> example in my single-node setup Hadoop 2.2.0 + ZooKeeper 3.4.5:
> > >>         mkdir test_example
> > >>         ln -s
> > >>         $GIRAPH_PREFIX/giraph-examples/target/giraph-examples-1.1.0-
> > >>
> > >> SNAPSHOT-for-hadoop-2.2.0-jar-with-dependencies.jar
> > >>
> > >>         $HADOOP_PREFIX/bin/hadoop jar
> giraph-examples-1.1.0-SNAPSHOT-for-
> > >>
> > >> hadoop-2.2.0-jar-with-dependencies.jar org.apache.giraph.GiraphRunner
> > >> org.apache.giraph.examples.SimpleShortestPathsComputation -vif
> > >>
> org.apache.giraph.io.formats.JsonLongDoubleFloatDoubleVertexInputFormat
> > >> -vip
> > >> giraph/input/tiny_graph.txt -vof
> > >> org.apache.giraph.io.formats.IdWithValueTextOutputFormat -op
> > >> giraph/output/shortestpaths -w 1 -ca giraph.SplitMasterWorker=false
> -ca
> > >> giraph.zkList=localhost:2181 -yj giraph-examples-1.1.0-SNAPSHOT-for-
> > >> hadoop-2.2.0-jar-with-dependencies.jar
> > >>
> > >> ###########
> > >> Notes:
> > >> * Wasn't able to do mvn package as it complained about not having the
> > >> dependencies giraph-hive, giraph-hbase, etc... I suspect this is just
> a
> > >> matter
> > >> of changing the main pom.xml to include those modules with the hadoop
> > >> 2.2.0
> > >> target or remove those dependencies from the giraph-dist if they no
> > >> longer
> > >> apply.
> > >> * You may get some memory limit exceeded problems for the
> > >> ApplicationMaster.
> > >> To fix, either increase the yarn.nodemanager.vmem-pmem-ratio
> parameter in
> > >> yarn-
> > >> site.xml or apply my patch to prevent allocation of heap size equal to
> > >> total
> > >> memory size, described at:
> > >> https://issues.apache.org/jira/browse/GIRAPH-812
> > >> * In my case, the application didn't exit even after outputting the
> > >> result and
> > >> having recognized that all nodes voted to terminate. I've opened an
> issue
> > >> in JIRA regarding this so if you suffer from the same, you can apply
> that
> > >> patch
> > >> too: https://issues.apache.org/jira/browse/GIRAPH-811
> > >>
> > >> ###########
> > >> Relevant JIRA issues:
> > >> * https://issues.apache.org/jira/browse/GIRAPH-798
> > >> * https://issues.apache.org/jira/browse/GIRAPH-804
> > >> * https://issues.apache.org/jira/browse/GIRAPH-811
> > >> * https://issues.apache.org/jira/browse/GIRAPH-812
> > >>
> > >> Best regards,
> > >> Alexandre
> > >>
> > >> On Friday 06 December 2013 00:32:32 Yong Guo wrote:
> > >> > Hi,
> > >> >
> > >> > I also got this error when tried to build Giraph on top of
> hadoop-2.2.0
> > >> > using similar commands. Can anyone help?
> > >> >
> > >> > Thanks,
> > >> > Yong
> > >> >
> > >> >
> > >> > 2013/12/6 Rohit Bhat <rohitbhat.nitk@gmail.com>
> > >> >
> > >> > > I already have yarn (hadoop_2.2.0) on my machine. I tried the
> > >>
> > >> following 2
> > >>
> > >> > > commands and got similar errors in both the cases:
> > >> > >
> > >> > > 1. "mvn -Phadoop_yarn -Dhadoop.version=2.2.0 -X clean package
> > >>
> > >> -DskipTests"
> > >>
> > >> > > 2. "mvn -P2.2.0 -DskipTests -Dmaven.javadoc.skip=true clean
> install
> > >> > > package"
> > >> > >
> > >> > >
> > >> > > [INFO] Checking dependency versions
> > >> > >
> > >> > > [ERROR] Found a problem with the direct dependency
> > >> > > commons-httpclient:commons-httpclient of the current project
> > >> > >
> > >> > >   Expected version is 3.0.1
> > >> > >
> > >> > >   Resolved version is 3.0.1
> > >>
> > >> > >   Version 3.1 was expected by artifact:
> > >> org.apache.hadoop:hadoop-common
> > >>
> > >> > > [ERROR] Found a problem with the dependency
> commons-lang:commons-lang
> > >> > >
> > >> > >   Resolved version is 2.4
> > >> > >
> > >> > >   Version 2.4 was expected by artifact:
> > >> > > commons-configuration:commons-configuration
> > >> > >
> > >> > >   Version 2.5 was expected by artifact:
> > >> org.apache.hadoop:hadoop-common
> > >>
> > >> > > [ERROR] Found a problem with the dependency
> > >> > > commons-logging:commons-logging
> > >> > >
> > >> > >   Resolved version is 1.0.4
> > >>
> > >> > >   Version 1.1.1 was expected by artifact:
> > >> org.apache.hadoop:hadoop-common
> > >>
> > >> > > [ERROR] Found a problem with the dependency io.netty:netty
> > >> > >
> > >> > >   Resolved version is 3.5.3.Final
> > >> > >
> > >> > >   Version 3.6.2.Final was expected by artifacts: org.apache.
> > >> > >
> > >> > > hadoop:hadoop-mapreduce-client-common, org.apache.
> > >> > > hadoop:hadoop-mapreduce-client-core
> > >> > >
> > >> > > [ERROR] Found a problem with the dependency
> > >>
> > >> org.apache.zookeeper:zookeeper
> > >>
> > >> > >   Resolved version is 3.3.3
> > >> > >
> > >> > >   Version 3.4.5 was expected by artifacts:
> > >> > >   org.apache.hadoop:hadoop-common,
> > >> > >
> > >> > > org.apache.hadoop:hadoop-mapreduce-client-common
> > >> > >
> > >> > >
> > >> > > Am i missing something?
> > >> > >
> > >> > > On Mon, Dec 2, 2013 at 7:21 PM, Ameya Vilankar
> > >>
> > >> <ameya.vilankar@gmail.com>wrote:
> > >> > >> Yes. Use this:
> > >> > >>
> > >> > >> mvn -Phadoop_cdh4.4.0 -DskipTests -Dmaven.javadoc.skip=true
> package
> > >> > >>
> > >> > >> On Mon, Dec 2, 2013 at 5:18 PM, Manuel Lagang
> > >>
> > >> <manuellagang@gmail.com>wrote:
> > >> > >>> I get the same error when I compile Giraph against the
default
> > >>
> > >> hadoop
> > >>
> > >> > >>> version (0.20.203.0), but my project that uses Giraph
uses a
> more
> > >> > >>> recent hadoop version. Did you set the hadoop version
via a
> maven
> > >> > >>> profile
> > >> > >>> when compiling Giraph (e.g. mvn -Phadoop_1.0 compile
for hadoop
> > >>
> > >> 1.0)?
> > >>
> > >> > >>> Presumably, there's a way to compile Giraph for Yarn.
There's
> even
> > >> > >>> a
> > >> > >>> Yarn profile in the pom.xml. I personally haven't had
success
> > >>
> > >> building
> > >>
> > >> > >>> it
> > >> > >>> though.
> > >> > >>>
> > >> > >>> On Mon, Dec 2, 2013 at 4:30 PM, Rohit Bhat
> > >>
> > >> <rohitbhat.nitk@gmail.com>wrote:
> > >> > >>>> Hi,
> > >> > >>>>
> > >> > >>>> I am new to Giraph. I have installed Yarn (hadoop
2.2.0) and
> have
> > >> > >>>> installed Giraph on top of it. I have been trying
to
> > >> > >>>> execute SimpleShortestPathsComputation example but
i am getting
> > >> > >>>> the
> > >> > >>>> error:
> > >>
> > >> > >>>> "java.lang.IllegalArgumentException:
> > >> checkLocalJobRunnerConfiguration:
> > >> > >>>> When using LocalJobRunner, you cannot run in split
master /
> worker
> > >>
> > >> mode
> > >>
> > >> > >>>> since there is only 1 task at a time!"
> > >> > >>>>
> > >> > >>>> I fixed this by adding an entry in mapred-site.xml
for
> > >> > >>>> mapreduce.jobtracker.address but now i am getting
a different
> > >>
> > >> error:
> > >> > >>>> *Exception in thread "main"
> > >> > >>>> java.lang.IncompatibleClassChangeError:
> > >> > >>>> Found interface org.apache.hadoop.mapreduce.JobContext,
but
> class
> > >>
> > >> was
> > >>
> > >> > >>>> expected*
> > >> > >>>>
> > >> > >>>>  at
> > >>
> > >>
> org.apache.giraph.bsp.BspOutputFormat.checkOutputSpecs(BspOutputFormat.
> > >>
> > >> > >>>> java:43) at
> > >>
> > >>
> org.apache.hadoop.mapreduce.JobSubmitter.checkSpecs(JobSubmitter.java:4
> > >>
> > >> > >>>> 56)
> > >> > >>>>
> > >> > >>>>  at
> > >>
> > >>
> org.apache.hadoop.mapreduce.JobSubmitter.submitJobInternal(JobSubmitter
> > >>
> > >> > >>>> .java:342) at
> > >> > >>>> org.apache.hadoop.mapreduce.Job$10.run(Job.java:1268)
> > >> > >>>>
> > >> > >>>>  at org.apache.hadoop.mapreduce.Job$10.run(Job.java:1265)
> > >> > >>>>
> > >> > >>>> at java.security.AccessController.doPrivileged(Native
Method)
> > >> > >>>>
> > >> > >>>>  at javax.security.auth.Subject.doAs(Subject.java:415)
> > >> > >>>>
> > >> > >>>> at
> > >>
> > >>
> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformati
> > >>
> > >> > >>>> on.java:1491)>>>>
> > >> > >>>>
> > >> > >>>>  at org.apache.hadoop.mapreduce.Job.submit(Job.java:1265)
> > >> > >>>>
> > >> > >>>> at org.apache.giraph.job.GiraphJob.run(GiraphJob.java:250)
> > >> > >>>>
> > >> > >>>>  at org.apache.giraph.GiraphRunner.run(GiraphRunner.java:94)
> > >> > >>>>
> > >> > >>>> at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:70)
> > >> > >>>>
> > >> > >>>>  at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:84)
> > >> > >>>>
> > >> > >>>> at org.apache.giraph.GiraphRunner.main(GiraphRunner.java:124)
> > >> > >>>>
> > >> > >>>>  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
> > >> > >>>>
> > >> > >>>> at
> > >>
> > >>
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.ja
> > >>
> > >> > >>>> va:57)>>>>
> > >> > >>>>
> > >> > >>>>  at
> > >>
> > >>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso
> > >>
> > >> > >>>> rImpl.java:43) at
> java.lang.reflect.Method.invoke(Method.java:606)
> > >> > >>>>
> > >> > >>>>  at org.apache.hadoop.util.RunJar.main(RunJar.java:212)
> > >> > >>>>
> > >> > >>>> *Is Giraph compatible with yarn? If yes, am i missing
> anything?*
> > >> > >>>>
> > >> > >>>> Thanks,
> > >> > >>>> Rohit
>

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