Amazon EMR: running Custom Jar with input and output from S3

Question

I am trying to run an EMR cluster which has a custom jar step. The program takes input from S3 and outputs to S3 (or at least this is what I want to accomplish). In the step configuration, I have the following in the arguments field:

v3.MaxTemperatureDriver
s3n://hadoopbook/ncdc/all
s3n://hadoop-szhu/max-temp

where hadoopbook/ncdc/all is the path to the bucket containing the input data (as a side note, the example I'm running is from this book), and hadoop-szhu is my own bucket where I want to store the output. Following this post, my MapReduce driver looks like this:

package v3;

import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;

import v1.MaxTemperatureReducer;

public class MaxTemperatureDriver extends Configured implements Tool {

  @Override
  public int run(String[] args) throws Exception {
    if (args.length != 2) {
      System.err.printf("Usage: %s [generic options] <input> <output>\n",
          getClass().getSimpleName());
      ToolRunner.printGenericCommandUsage(System.err);
      return -1;
    }

    Job job = new Job(getConf(), "Max temperature");
    job.setJarByClass(getClass());

    FileInputFormat.addInputPath(job, new Path(args[0]));
    FileOutputFormat.setOutputPath(job, new Path(args[1]));

    job.setMapperClass(MaxTemperatureMapper.class);
    job.setCombinerClass(MaxTemperatureReducer.class);
    job.setReducerClass(MaxTemperatureReducer.class);

    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(IntWritable.class);

    return job.waitForCompletion(true) ? 0 : 1;
  }

  public static void main(String[] args) throws Exception {
    int exitCode = ToolRunner.run(new MaxTemperatureDriver(), args);
    System.exit(exitCode);
  }
}

However, when I try to run this, I get the following error:

Exception in thread "main" java.io.IOException: No FileSystem for scheme: s3n

I've also tried to copy the data from s3 to the cluster using the following (run after sshing into the master node):

hadoop distcp \
  -Dfs.s3n.awsAccessKeyId='...' \
  -Dfs.s3n.awsSecretAccessKey='...' \
  s3n://hadoopbook/ncdc/all input/ncdc/all

But I get a bunch of errors, I've included an excerpt below:

2016-09-03 07:07:11,858 FATAL [IPC Server handler 6 on 43495] org.apache.hadoop.mapred.TaskAttemptListenerImpl: Task: attempt_1472884232220_0001_m_000000_0 - exited : java.io.IOException: org.apache.hadoop.tools.mapred.RetriableFileCopyCommand$CopyReadException: java.io.FileNotFoundException: No such file or directory 's3n://hadoopbook/ncdc/all/1901.gz'
    at org.apache.hadoop.tools.mapred.CopyMapper.map(CopyMapper.java:224)
    at org.apache.hadoop.tools.mapred.CopyMapper.map(CopyMapper.java:50)
    at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:146)
    at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:796)
    at org.apache.hadoop.mapred.MapTask.run(MapTask.java:342)
    at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:164)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.security.auth.Subject.doAs(Subject.java:422)
    at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
    at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:158)
Caused by: org.apache.hadoop.tools.mapred.RetriableFileCopyCommand$CopyReadException: java.io.FileNotFoundException: No such file or directory 's3n://hadoopbook/ncdc/all/1901.gz'
    ... 10 more
Caused by: java.io.FileNotFoundException: No such file or directory 's3n://hadoopbook/ncdc/all/1901.gz'
    at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.getFileStatus(S3NativeFileSystem.java:818)
    at com.amazon.ws.emr.hadoop.fs.EmrFileSystem.getFileStatus(EmrFileSystem.java:511)
    at org.apache.hadoop.tools.mapred.CopyMapper.map(CopyMapper.java:219)
    ... 9 more

I'm not sure where the issue lies, but I would be happy to include more details (please comment below). Thanks!

Answer 1

s3n:// is the old protocol, you should instead be using s3://

Reference: http://docs.aws.amazon.com//ElasticMapReduce/latest/ManagementGuide/emr-plan-file-systems.html