Skip to main content

A tricky exception running MapReduce functions through RHadoop: root cause and how to fix it.

RHadoop (https://github.com/RevolutionAnalytics/RHadoop/wiki) is a collection of five R packages (rhdfs, rmr2, rhbase, ravro, plyrmr) that allow users to manage and analyze data with Hadoop. Running any MapReduce function, also this simple one

    from.dfs(mapreduce(to.dfs(1:100))) 

through RHadoop on Linux servers you could face this exception:

2015-10-20 08:39:41,722 ERROR [main] org.apache.hadoop.streaming.PipeMapRed: configuration exception
java.io.IOException: Cannot run program "Rscript": error=2, No such file or directory
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1059)
    at org.apache.hadoop.streaming.PipeMapRed.configure(PipeMapRed.java:209)
    at org.apache.hadoop.streaming.PipeMapper.configure(PipeMapper.java:66)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:95)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:56)
    at java.lang.reflect.Method.invoke(Method.java:620)
    at org.apache.hadoop.util.ReflectionUtils.setJobConf(ReflectionUtils.java:109)
    at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:78)
    at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:136)
    at org.apache.hadoop.mapred.MapRunner.configure(MapRunner.java:38)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:95)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:56)
    at java.lang.reflect.Method.invoke(Method.java:620)
    at org.apache.hadoop.util.ReflectionUtils.setJobConf(ReflectionUtils.java:109)
    at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:78)
    at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:136)
    at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:449)
    at org.apache.hadoop.mapred.MapTask.run(MapTask.java:343)
    at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:164)
    at java.security.AccessController.doPrivileged(AccessController.java:452)
    at javax.security.auth.Subject.doAs(Subject.java:572)
    at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
    at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)
Caused by: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:188)
    at java.lang.ProcessImpl.start(ProcessImpl.java:164)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1040)
    ... 24 more
   
At first glance one could think of a missing permission issue on the Rscript tool for the user running Hadoop (the file cannot be missing because it is part of the R environment and the MapReduce function has been triggered by a R console). But this issue happens also when the permissions for that user are r-x for the Rscript file. The root cause for this issue is the following: RHadoop/Hadoop tries to to execute the Rscript tool from the /usr/bin/ location when it is really in the $R_HOME/bin/ directory. The solution is simple. As root user create a symbolic link to the Rscript file this way:

ln -s $R_HOME/bin/Rscript /usr/bin/Rscript

This solution works on Red Hat and CentOS, but I suppose it should work on any Linux distro.
Labels:

Comments

Post a Comment

Popular posts from this blog

Exporting InfluxDB data to a CVS file

Sometimes you would need to export a sample of the data from an InfluxDB table to a CSV file (for example to allow a data scientist to do some offline analysis using a tool like Jupyter, Zeppelin or Spark Notebook). It is possible to perform this operation through the influx command line client. This is the general syntax: sudo /usr/bin/influx -database '<database_name>' -host '<hostname>' -username '<username>'  -password '<password>' -execute 'select_statement' -format '<format>' > <file_path>/<file_name>.csv where the format could be csv , json or column . Example: sudo /usr/bin/influx -database 'telegraf' -host 'localhost' -username 'admin'  -password '123456789' -execute 'select * from mem' -format 'csv' > /home/googlielmo/influxdb-export/mem-export.csv
6 comments
Read more

jOOQ: code generation in Eclipse

jOOQ allows code generation from a database schema through ANT tasks, Maven and shell command tools. But if you're working with Eclipse it's easier to create a new Run Configuration to perform this operation. First of all you have to write the usual XML configuration file for the code generation starting from the database: <?xml version="1.0" encoding="UTF-8" standalone="yes"?> <configuration xmlns="http://www.jooq.org/xsd/jooq-codegen-2.0.4.xsd">   <jdbc>     <driver>oracle.jdbc.driver.OracleDriver</driver>     <url>jdbc:oracle:thin:@dbhost:1700:DBSID</url>     <user>DB_FTRS</user>     <password>password</password>   </jdbc>   <generator>     <name>org.jooq.util.DefaultGenerator</name>     <database>       <name>org.jooq.util.oracle.OracleDatabase</name>     ...
Post a Comment
Read more

Using Rapids cuDF in a Colab notebook

During last Spark+AI Summit Europe 2019 I had a chance to attend a talk from Miguel Martinez  who was presenting Rapids , the new Open Source framework from NVIDIA for GPU accelerated end-to-end Data Science and Analytics. Fig. 1 - Overview of the Rapids eco-system Rapids is a suite of Open Source libraries: cuDF cuML cuGraph cuXFilter I enjoied the presentation and liked the idea of this initiative, so I wanted to start playing with the Rapids libraries in Python on Colab , starting from cuDF, but the first attempt came with an issue that I eventually solved. So in this post I am going to share how I fixed it, with the hope it would be useful to someone else running into the same blocker. I am assuming here you are already familiar with Google Colab. I am using Python 3.x as Python 2 isn't supported by Rapids. Once you have created a new notebook in Colab, you need to check if the runtime for it is set to use Python 3 and uses a GPU as hardware accelerator. You...
5 comments
Read more