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POExecute jar file using hadoop
 

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  1. POExecute jar file using hadoop
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    <p>I want to execute a jar file which works fine upon executing from command line:</p> <pre><code>java -Xmx3g -jar jarname.jar -T class_name_in_jar -R filename1 -I filename2 -known filename3 -o filename4 </code></pre> <p>Above command executes *class_name_in_jar* by taking input filename1, filename2 and filename3. it will generate output in filename4.</p> <p>Here is my map reduce program:</p> <pre><code>import java.io.IOException; import java.util.*; import org.apache.hadoop.fs.Path; import org.apache.hadoop.conf.*; import org.apache.hadoop.io.*; import org.apache.hadoop.mapred.*; import org.apache.hadoop.util.*; public class GatkWordCount { public static class Reduce extends MapReduceBase implements Reducer&lt;Text, IntWritable, Text, IntWritable&gt; { public void reduce(Text key, Iterator&lt;IntWritable&gt; values, OutputCollector&lt;Text, IntWritable&gt; output, Reporter reporter) throws IOException { String find_targets_cmd = "java -Xmx3g -jar &lt;jarname&gt;.jar -T &lt;class name in jar&gt; -R &lt;filename1&gt; -I &lt;filename2&gt; -known &lt;filename3&gt; -o &lt;filename4&gt;"; exceptionOnError(execAndReconnect(find_targets_cmd)); } } public static int execAndReconnect(String cmd) throws IOException { Process p = Runtime.getRuntime().exec(cmd); p.waitFor(); return p.exitValue(); } public static void exceptionOnError(int errorCode) throws IOException{ if(0 != errorCode) throw new IOException(String.valueOf(errorCode)); } public static void main(String[] args) throws Exception { JobConf conf = new JobConf(GatkWordCount.class); conf.setJobName("GatkWordCount"); conf.setOutputKeyClass(Text.class); conf.setOutputValueClass(IntWritable.class); conf.setReducerClass(Reduce.class); conf.setInputFormat(TextInputFormat.class); conf.setOutputFormat(TextOutputFormat.class); FileInputFormat.setInputPaths(conf, new Path(args[0])); FileOutputFormat.setOutputPath(conf, new Path(args[1])); JobClient.runJob(conf); } } </code></pre> <hr> <p>In <code>HDFS</code>, I have put all the required input files. I have executed below command:</p> <pre><code> enter code herehadoop/bin/hadoop jar gatkword.jar GatkWordCount /user/hduser/gatkinput/gatkinput/group.bam /user/hduser/gatkword2 </code></pre> <p>Below is the error message am getting after executing above command:</p> <pre><code>13/12/29 17:58:59 WARN mapred.JobClient: Use GenericOptionsParser for parsing the arguments. Applications should implement Tool for the same. 13/12/29 17:58:59 INFO util.NativeCodeLoader: Loaded the native-hadoop library 13/12/29 17:58:59 WARN snappy.LoadSnappy: Snappy native library not loaded 13/12/29 17:58:59 INFO mapred.FileInputFormat: Total input paths to process : 1 13/12/29 17:58:59 INFO mapred.JobClient: Running job: job_201312261425_0013 13/12/29 17:59:00 INFO mapred.JobClient: map 0% reduce 0% 13/12/29 17:59:06 INFO mapred.JobClient: Task Id : attempt_201312261425_0013_m_000000_0, Status : FAILED java.io.IOException: Type mismatch in key from map: expected org.apache.hadoop.io.Text, recieved org.apache.hadoop.io.LongWritable at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.collect(MapTask.java:1014) at org.apache.hadoop.mapred.MapTask$OldOutputCollector.collect(MapTask.java:592) at org.apache.hadoop.mapred.lib.IdentityMapper.map(IdentityMapper.java:38) at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:50) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:436) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:372) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1136) at org.apache.hadoop.mapred.Child.main(Child.java:249) 13/12/29 17:59:06 INFO mapred.JobClient: Task Id : attempt_201312261425_0013_m_000001_0, Status : FAILED java.io.IOException: Type mismatch in key from map: expected org.apache.hadoop.io.Text, recieved org.apache.hadoop.io.LongWritable at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.collect(MapTask.java:1014) at org.apache.hadoop.mapred.MapTask$OldOutputCollector.collect(MapTask.java:592) at org.apache.hadoop.mapred.lib.IdentityMapper.map(IdentityMapper.java:38) at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:50) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:436) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:372) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1136) at org.apache.hadoop.mapred.Child.main(Child.java:249) 13/12/29 17:59:11 INFO mapred.JobClient: Task Id : attempt_201312261425_0013_m_000000_1, Status : FAILED java.io.IOException: Type mismatch in key from map: expected org.apache.hadoop.io.Text, recieved org.apache.hadoop.io.LongWritable at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.collect(MapTask.java:1014) at org.apache.hadoop.mapred.MapTask$OldOutputCollector.collect(MapTask.java:592) at org.apache.hadoop.mapred.lib.IdentityMapper.map(IdentityMapper.java:38) at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:50) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:436) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:372) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1136) at org.apache.hadoop.mapred.Child.main(Child.java:249) 13/12/29 17:59:11 INFO mapred.JobClient: Task Id : attempt_201312261425_0013_m_000001_1, Status : FAILED java.io.IOException: Type mismatch in key from map: expected org.apache.hadoop.io.Text, recieved org.apache.hadoop.io.LongWritable at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.collect(MapTask.java:1014) at org.apache.hadoop.mapred.MapTask$OldOutputCollector.collect(MapTask.java:592) at org.apache.hadoop.mapred.lib.IdentityMapper.map(IdentityMapper.java:38) at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:50) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:436) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:372) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1136) at org.apache.hadoop.mapred.Child.main(Child.java:249) 13/12/29 17:59:17 INFO mapred.JobClient: Task Id : attempt_201312261425_0013_m_000000_2, Status : FAILED java.io.IOException: Type mismatch in key from map: expected org.apache.hadoop.io.Text, recieved org.apache.hadoop.io.LongWritable at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.collect(MapTask.java:1014) at org.apache.hadoop.mapred.MapTask$OldOutputCollector.collect(MapTask.java:592) at org.apache.hadoop.mapred.lib.IdentityMapper.map(IdentityMapper.java:38) at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:50) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:436) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:372) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1136) at org.apache.hadoop.mapred.Child.main(Child.java:249) 13/12/29 17:59:17 INFO mapred.JobClient: Task Id : attempt_201312261425_0013_m_000001_2, Status : FAILED java.io.IOException: Type mismatch in key from map: expected org.apache.hadoop.io.Text, recieved org.apache.hadoop.io.LongWritable at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.collect(MapTask.java:1014) at org.apache.hadoop.mapred.MapTask$OldOutputCollector.collect(MapTask.java:592) at org.apache.hadoop.mapred.lib.IdentityMapper.map(IdentityMapper.java:38) at org.apache.hadoop.mapred.MapRunner.run(MapRunner.java:50) at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:436) at org.apache.hadoop.mapred.MapTask.run(MapTask.java:372) at org.apache.hadoop.mapred.Child$4.run(Child.java:255) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:415) at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1136) at org.apache.hadoop.mapred.Child.main(Child.java:249) 13/12/29 17:59:22 INFO mapred.JobClient: Job complete: job_201312261425_0013 13/12/29 17:59:22 INFO mapred.JobClient: Counters: 7 13/12/29 17:59:22 INFO mapred.JobClient: Job Counters 13/12/29 17:59:22 INFO mapred.JobClient: SLOTS_MILLIS_MAPS=42572 13/12/29 17:59:22 INFO mapred.JobClient: Total time spent by all reduces waiting after reserving slots (ms)=0 13/12/29 17:59:22 INFO mapred.JobClient: Total time spent by all maps waiting after reserving slots (ms)=0 13/12/29 17:59:22 INFO mapred.JobClient: Launched map tasks=8 13/12/29 17:59:22 INFO mapred.JobClient: Data-local map tasks=8 13/12/29 17:59:22 INFO mapred.JobClient: SLOTS_MILLIS_REDUCES=0 13/12/29 17:59:22 INFO mapred.JobClient: Failed map tasks=1 13/12/29 17:59:22 INFO mapred.JobClient: Job Failed: # of failed Map Tasks exceeded allowed limit. FailedCount: 1. LastFailedTask: task_201312261425_0013_m_000000 Exception in thread "main" java.io.IOException: Job failed! at org.apache.hadoop.mapred.JobClient.runJob(JobClient.java:1327) at GatkWordCount.main(GatkWordCount.java:51) 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:601) at org.apache.hadoop.util.RunJar.main(RunJar.java:156) </code></pre> <p>Please suggest what needs to be change in my code in order to execute it properly. Thanks for your help.</p>
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