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From Ethan Xu <ethan.yifa...@gmail.com>
Subject Re: Compatibility with MR1 Cloudera cdh4.2.1
Date Fri, 05 Feb 2016 14:47:49 GMT
Thank you Shirish and Deron for the suggestions. Looking forward to the fix
from Matthias!

We are using the hadoop-common shipped with CDH4.2.1, and it's in
classpath. I'm a bit hesitate to alter our hadoop configuration to include
other versions since other people are using it too.

Not sure if/how the following naive approach affects the program behavior,
but I did try changing the scope of

<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-common</artifactId>
<version>${hadoop.version}</version>

in SystemML's pom.xml from 'provided' to 'compile' and rebuilt the jar
(21MB), and it threw the same error.

By the way this is in pom.xml line 65 - 72:
<properties>
          <hadoop.version>2.4.1</hadoop.version>
          <antlr.version>4.3</antlr.version>
          <spark.version>1.4.1</spark.version>

                <!-- OS-specific JVM arguments for running integration
tests -->
                <integrationTestExtraJVMArgs />
</properties>

Am I supposed to modify the hadoop.version before build?

Thanks again,

Ethan



On Fri, Feb 5, 2016 at 2:29 AM, Deron Eriksson <deroneriksson@gmail.com>
wrote:

> Hi Matthias,
>
> Glad to hear the fix is simple. Mixing jar versions sometimes is not very
> fun.
>
> Deron
>
>
> On Thu, Feb 4, 2016 at 11:10 PM, Matthias Boehm <mboehm@us.ibm.com> wrote:
>
> > well, let's not mix different hadoop versions in the class path or
> > client/server. If I'm not mistaken, cdh 4.x always shipped with MR v1.
> It's
> > a trivial fix for us and will be in the repo tomorrow morning anyway.
> > Thanks for catching this issue Ethan.
> >
> > Regards,
> > Matthias
> >
> > [image: Inactive hide details for Deron Eriksson ---02/04/2016 11:04:38
> > PM---Hi Ethan, Just FYI, I looked at hadoop-common-2.0.0-cdh4.2]Deron
> > Eriksson ---02/04/2016 11:04:38 PM---Hi Ethan, Just FYI, I looked at
> > hadoop-common-2.0.0-cdh4.2.1.jar (
> >
> > From: Deron Eriksson <deroneriksson@gmail.com>
> > To: dev@systemml.incubator.apache.org
> > Date: 02/04/2016 11:04 PM
> > Subject: Re: Compatibility with MR1 Cloudera cdh4.2.1
> > ------------------------------
> >
> >
> >
> > Hi Ethan,
> >
> > Just FYI, I looked at hadoop-common-2.0.0-cdh4.2.1.jar (
> >
> >
> https://repository.cloudera.com/artifactory/repo/org/apache/hadoop/hadoop-common/2.0.0-cdh4.2.1/
> > ),
> > since I don't see a 2.0.0-mr1-cdh4.2.1 version, and the
> > org.apache.hadoop.conf.Configuration class in that jar doesn't appear to
> > have a getDouble method, so using that version of hadoop-common won't
> work.
> >
> > However, the hadoop-common-2.4.1.jar (
> >
> >
> https://repository.cloudera.com/artifactory/repo/org/apache/hadoop/hadoop-common/2.4.1/
> > )
> >
> > does appear to have the getDouble method. It's possible that adding that
> > jar to your classpath may fix your problem, as Shirish pointed out.
> >
> > It sounds like Matthias may have another fix.
> >
> > Deron
> >
> >
> >
> > On Thu, Feb 4, 2016 at 6:40 PM, Matthias Boehm <mboehm@us.ibm.com>
> wrote:
> >
> > > well, we did indeed not run on MR v1 for a while now. However, I don't
> > > want to get that far and say we don't support it anymore. I'll fix this
> > > particular issue by tomorrow.
> > >
> > > In the next couple of weeks we should run our full performance
> testsuite
> > > (for broad coverage) over an MR v1 cluster and systematically remove
> > > unnecessary incompatibility like this instance. Any volunteers?
> > >
> > > Regards,
> > > Matthias
> > >
> > > [image: Inactive hide details for Ethan Xu ---02/04/2016 05:51:28
> > > PM---Hello, I got an error when running the
> > systemML/scripts/Univar-S]Ethan
> > > Xu ---02/04/2016 05:51:28 PM---Hello, I got an error when running the
> > > systemML/scripts/Univar-Stats.dml script on
> > >
> > > From: Ethan Xu <ethan.yifanxu@gmail.com>
> > > To: dev@systemml.incubator.apache.org
> > > Date: 02/04/2016 05:51 PM
> > > Subject: Compatibility with MR1 Cloudera cdh4.2.1
> > > ------------------------------
> >
> > >
> > >
> > >
> > > Hello,
> > >
> > > I got an error when running the systemML/scripts/Univar-Stats.dml
> script
> > on
> > > a hadoop cluster (Cloudera CDH4.2.1) on a 6GB data set. Error message
> is
> > at
> > > the bottom of the email. The same script ran fine on a smaller sample
> > > (several MB) of the same data set, when MR was not invoked.
> > >
> > > The main error was java.lang.NoSuchMethodError:
> > > org.apache.hadoop.mapred.JobConf.getDouble()
> > > Digging deeper, it looks like the CDH4.2.1 version of MR indeed didn't
> > have
> > > the JobConf.getDouble() method.
> > >
> > > The hadoop-core jar of CDH4.2.1 can be found here:
> > >
> > >
> >
> >
> https://repository.cloudera.com/artifactory/repo/org/apache/hadoop/hadoop-core/2.0.0-mr1-cdh4.2.1/
> >
> > >
> > > The calling line of SystemML is line 1194 of
> > >
> > >
> >
> https://github.com/apache/incubator-systemml/blob/master/src/main/java/org/apache/sysml/runtime/matrix/mapred/MRJobConfiguration.java
> > >
> > > I was wondering, if the finding is accurate, is there a potential fix,
> or
> > > does this mean the current version of SystemML is not compatible with
> > > CDH4.2.1?
> > >
> > > Thank you,
> > >
> > > Ethan
> > >
> > >
> > > hadoop jar $sysDir/target/SystemML.jar -f
> > > $sysDir/scripts/algorithms/Univar-Stats.dml -nvargs
> > > X=$baseDirHDFS/original-coded.csv
> > > TYPES=$baseDirHDFS/original-coded-type.csv
> > > STATS=$baseDirHDFS/univariate-summary.csv
> > >
> > > 16/02/04 20:35:03 INFO api.DMLScript: BEGIN DML run 02/04/2016 20:35:03
> > > 16/02/04 20:35:03 INFO api.DMLScript: HADOOP_HOME: null
> > > 16/02/04 20:35:03 WARN conf.DMLConfig: No default SystemML config file
> > > (./SystemML-config.xml) found
> > > 16/02/04 20:35:03 WARN conf.DMLConfig: Using default settings in
> > DMLConfig
> > > 16/02/04 20:35:04 WARN hops.OptimizerUtils: Auto-disable multi-threaded
> > > text read for 'text' and 'csv' due to thread contention on JRE < 1.8
> > > (java.version=1.7.0_71).
> > > SLF4J: Class path contains multiple SLF4J bindings.
> > > SLF4J: Found binding in
> > >
> > >
> >
> [jar:file:/usr/lib/zookeeper/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> > > SLF4J: Found binding in
> > >
> > >
> >
> [jar:file:/usr/local/explorys/datagrid/lib/slf4j-jdk14-1.6.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> > > SLF4J: Found binding in
> > >
> > >
> >
> [jar:file:/usr/local/explorys/datagrid/lib/logback-classic-1.0.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> > > SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an
> > > explanation.
> > > 16/02/04 20:35:07 INFO api.DMLScript: SystemML Statistics:
> > > Total execution time:        0.880 sec.
> > > Number of executed MR Jobs:    0.
> > >
> > > 16/02/04 20:35:07 INFO api.DMLScript: END DML run 02/04/2016 20:35:07
> > > Exception in thread "main" java.lang.NoSuchMethodError:
> > > org.apache.hadoop.mapred.JobConf.getDouble(Ljava/lang/String;D)D
> > >    at
> > >
> > >
> >
> org.apache.sysml.runtime.matrix.mapred.MRJobConfiguration.setUpMultipleInputs(MRJobConfiguration.java:1195)
> > >    at
> > >
> > >
> >
> org.apache.sysml.runtime.matrix.mapred.MRJobConfiguration.setUpMultipleInputs(MRJobConfiguration.java:1129)
> > >    at
> > >
> > >
> >
> org.apache.sysml.runtime.matrix.CSVReblockMR.runAssignRowIDMRJob(CSVReblockMR.java:307)
> > >    at
> > >
> > >
> >
> org.apache.sysml.runtime.matrix.CSVReblockMR.runAssignRowIDMRJob(CSVReblockMR.java:289)
> > >    at
> > >
> >
> org.apache.sysml.runtime.matrix.CSVReblockMR.runJob(CSVReblockMR.java:275)
> > >    at
> > org.apache.sysml.lops.runtime.RunMRJobs.submitJob(RunMRJobs.java:257)
> > >    at
> > >
> > >
> >
> org.apache.sysml.lops.runtime.RunMRJobs.prepareAndSubmitJob(RunMRJobs.java:143)
> > >    at
> > >
> > >
> >
> org.apache.sysml.runtime.instructions.MRJobInstruction.processInstruction(MRJobInstruction.java:1500)
> > >    at
> > >
> > >
> >
> org.apache.sysml.runtime.controlprogram.ProgramBlock.executeSingleInstruction(ProgramBlock.java:309)
> > >    at
> > >
> > >
> >
> org.apache.sysml.runtime.controlprogram.ProgramBlock.executeInstructions(ProgramBlock.java:227)
> > >    at
> > >
> > >
> >
> org.apache.sysml.runtime.controlprogram.ProgramBlock.execute(ProgramBlock.java:169)
> > >    at
> > >
> org.apache.sysml.runtime.controlprogram.Program.execute(Program.java:146)
> > >    at org.apache.sysml.api.DMLScript.execute(DMLScript.java:676)
> > >    at org.apache.sysml.api.DMLScript.executeScript(DMLScript.java:338)
> > >    at org.apache.sysml.api.DMLScript.main(DMLScript.java:197)
> > >    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.hadoop.util.RunJar.main(RunJar.java:208)
> > >
> > >
> > >
> >
> >
> >
>



-- 
Yifan "Ethan" Xu, PhD

Data Scientist / Statistician
Explorys, IBM Watson Health

Adjunct Faculty
Department of Epidemiology and Biostatistics
Case Western Reserve University

--------------
Email: ethan.yifanxu@gmail.com
Phone: (607) 760-6817
--------------

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