not able to run the shell script with oozie - shell

Question

hi i am trying to run the shell script through oozie.while running the shell script i am getting the following error.
org.apache.oozie.action.hadoop.ShellMain], exit code [1]
my job.properties file
nameNode=hdfs://ip-172-31-41-199.us-west-2.compute.internal:8020
jobTracker=ip-172-31-41-199.us-west-2.compute.internal:8032
queueName=default
oozie.libpath=${nameNode}/user/oozie/share/lib/
oozie.use.system.libpath=true
oozie.wf.rerun.failnodes=true
oozieProjectRoot=shell_example
oozie.wf.application.path=${nameNode}/user/karun/${oozieProjectRoot}/apps/shell
my workflow.xml
<workflow-app xmlns="uri:oozie:workflow:0.1" name="pi.R example">
<start to="shell-node"/>
<action name="shell-node">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapred.job.queue.name</name>
<value>${queueName}</value>
</property>
</configuration>
<exec>script.sh</exec>
<file>/user/karun/oozie-oozi/script.sh#script.sh</file>
<capture-output/>
</shell>
<ok to="end"/>
<error to="fail"/>
</action>
<kill name="fail">
<message>Incorrect output</message>
</kill>
<end name="end"/>
</workflow-app>
my shell script- script.sh
export SPARK_HOME=/opt/cloudera/parcels/CDH-5.4.2-1.cdh5.4.2.p0.2/lib/spark
export YARN_CONF_DIR=/etc/hadoop/conf
export JAVA_HOME=/usr/java/jdk1.7.0_67-cloudera
export HADOOP_CMD=/usr/bin/hadoop
/SparkR-pkg/lib/SparkR/sparkR-submit --master yarn-client examples/pi.R yarn-client 4
error log file
WEBHCAT_DEFAULT_XML=/opt/cloudera/parcels/CDH-5.4.2- 1.cdh5.4.2.p0.2/etc/hive-webhcat/conf.dist/webhcat-default.xml:
CDH_KMS_HOME=/opt/cloudera/parcels/CDH-5.4.2-1.cdh5.4.2.p0.2/lib/hadoop-kms:
LANG=en_US.UTF-8:
HADOOP_MAPRED_HOME=/opt/cloudera/parcels/CDH-5.4.2- 1.cdh5.4.2.p0.2/lib/hadoop-mapreduce:
=================================================================
Invoking Shell command line now >>
Stdoutput Running /opt/cloudera/parcels/CDH-5.4.2-
1.cdh5.4.2.p0.2/lib/spark/bin/spark-submit --class edu.berkeley.cs.amplab.sparkr.SparkRRunner --files hdfs://ip-172-31-41-199.us-west-2.compute.internal:8020/user/karun/examples/pi.R --master yarn-client
/SparkR-pkg/lib/SparkR/sparkr-assembly-0.1.jar hdfs://ip-172-31-41-199.us-west- 2.compute.internal:8020/user/karun/examples/pi.R yarn-client 4
Stdoutput Fatal error: cannot open file 'pi.R': No such file or directory
Exit code of the Shell command 2
<<< Invocation of Shell command completed <<<
<<< Invocation of Main class completed <<<
Failing Oozie Launcher, Main class [org.apache.oozie.action.hadoop.ShellMain], exit code [1]
Oozie Launcher failed, finishing Hadoop job gracefully
Oozie Launcher, uploading action data to HDFS sequence file: hdfs://ip-172-31-41-199.us-west-2.compute.internal:8020/user/karun/oozie-oozi/0000035-150722003725443-oozie-oozi-W/shell-node--shell/action-data.seq
Oozie Launcher ends
I dont know how to solve the issue.any help will be appreciated.

Answer 1

sparkR-submit ... examples/pi.R ...
Fatal error: cannot open file 'pi.R': No such file or directory
The message is really explicit: your shell tries to read a R script from the local FileSystem. But local to what, actually???
Oozie uses YARN to run your shell; so YARN allocates a container on a random machine. It's something you must put into your head so that it becomes a reflex: all resources required by an Oozie Action (scripts, libraries, config files, whatever) must be
available in HDFS beforehand
downloaded at execution time thanks to <file> instructions in the Oozie script
accessed as local files in the Current Working Dir
In your case:
<exec>script.sh</exec>
<file>/user/karun/oozie-oozi/script.sh</file>
<file>/user/karun/some/place/pi.R</file>
Then
sparkR-submit ... pi.R ...