Reading file as single record in hadoop

Question

I have huge no. of small files, i want to use CombineFileInputFormat to merge the files such that each file data comes as a single record in my MR job. I have followed http://yaseminavcular.blogspot.in/2011/03/many-small-input-files.html and tried to convert it into the new api

I am facing 2 problems:

a) I am just testing it with 2 small files, still 2 mappers are fired. I expected 1

b) Each line is coming as single record, i want the whole file as single record.

It may be painful but please look into the code below. I am still a naive in hadoop

The driver class

public class MRDriver  extends Configured implements Tool {


@Override
public int run(String[] args) throws Exception {
    FileSystem fs = new Path(".").getFileSystem(getConf());
    fs.printStatistics();
    Job job = new Job(getConf());
    job.setJobName("Enron MR");
    job.setMapperClass(EnronMailReadMapper.class);
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(IntWritable.class);
    job.setNumReduceTasks(0);
    job.setJarByClass(EnronMailReadMapper.class);
    RawCombineFileInputFormat.addInputPath(job, new Path(args[0]));
    job.setOutputFormatClass(TextOutputFormat.class);
    TextOutputFormat.setOutputPath(job, new Path(args[1]));
    return job.waitForCompletion(true) ? 0 :1;  
}

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

}

The below class is mostly copy paste of LineRecordReader with modification to initialize() & nextKeyValue() function

public class SingleFileRecordReader extends RecordReader<LongWritable, Text> {
  private static final Log LOG = LogFactory.getLog(SingleFileRecordReader.class);

  private long start;
  private long pos;
  private long end;
  private LineReader in;
  private int maxLineLength;
  private LongWritable key = null;
  private Text value = null;

  public void initialize(InputSplit genericSplit,
                         TaskAttemptContext context) throws IOException {
    FileSplit split = (FileSplit) genericSplit;
    Configuration job = context.getConfiguration();
    this.maxLineLength = job.getInt("mapred.linerecordreader.maxlength",
                                    Integer.MAX_VALUE);
    start = split.getStart();
    end = start + split.getLength();
    final Path file = split.getPath();

    // open the file and seek to the start of the split
    FileSystem fs = file.getFileSystem(job);
    FSDataInputStream fileIn = fs.open(split.getPath());

      fileIn.seek(start);
      in = new LineReader(fileIn, job);
    // If this is not the first split, we always throw away first record
    // because we always (except the last split) read one extra line in
    // next() method.
    if (start != 0) {
      start += in.readLine(new Text(), 0, maxBytesToConsume(start));
    }
    this.pos = start;
  }

  private int maxBytesToConsume(long pos) {
    return (int) Math.min(Integer.MAX_VALUE, end - pos);
  }

  private long getFilePosition() throws IOException {
    long retVal= pos;
    return retVal;
  }

  public boolean nextKeyValue() throws IOException {
    if (key == null) {
      key = new LongWritable();
    }
    key.set(pos);
    if (value == null) {
      value = new Text();
    }
    int newSize = 0;
    StringBuffer totalValue = new StringBuffer();
    // We always read one extra line, which lies outside the upper
    // split limit i.e. (end - 1)
    while (getFilePosition() <= end) {
      newSize = in.readLine(value, maxLineLength,
          Math.max(maxBytesToConsume(pos), maxLineLength));
      if (newSize == 0) {
        break;
      }
      totalValue.append(value.toString()+"\n");
      pos += newSize;
      if (newSize < maxLineLength) {
        break;
      }

      // line too long. try again
      LOG.info("Skipped line of size " + newSize + " at pos " + 
               (pos - newSize));
    }
    if (newSize == 0) {
      key = null;
      value = null;
      return false;
    } else {
        value = new Text(totalValue.toString());
      return true;
    }
  }

  @Override
  public LongWritable getCurrentKey() {
    return key;
  }

  @Override
  public Text getCurrentValue() {
    return value;
  }

  /**
   * Get the progress within the split
   */
  public float getProgress() throws IOException {
    if (start == end) {
      return 0.0f;
    } else {
      return Math.min(1.0f,
        (getFilePosition() - start) / (float)(end - start));
    }
  }

  public synchronized void close() throws IOException {
    try {
      if (in != null) {
        in.close();
      }
    } finally {

    }
  }

}

Other files

public class RawCombineFileInputFormat extends CombineFileInputFormat <LongWritable,Text>{

@Override
public RecordReader<LongWritable, Text> createRecordReader(
        InputSplit split, TaskAttemptContext context) throws IOException {
    return new CombineFileRecordReader< LongWritable, Text >((CombineFileSplit) split, context, MultiFileRecordReader.class);
}

}

And

public class MultiFileRecordReader extends RecordReader < LongWritable, Text > {

 private CombineFileSplit split;
 private TaskAttemptContext context;
 private int index;
 private RecordReader< LongWritable, Text > rr;

public MultiFileRecordReader(CombineFileSplit split, TaskAttemptContext context, Integer index) {
    this.split = split;
    this.context = context;
    this.index = index;
    this.rr = new SingleFileRecordReader();
}
@Override
public void initialize(InputSplit split, TaskAttemptContext context)
        throws IOException, InterruptedException {
    this.split = (CombineFileSplit) split;
      this.context = context;

      if (null == rr) {
       rr = new SingleFileRecordReader();
      }

      FileSplit fileSplit = new FileSplit(this.split.getPath(index), 
                                          this.split.getOffset(index), 
                                          this.split.getLength(index), 
                                          this.split.getLocations());
      this.rr.initialize(fileSplit, this.context);

}

@Override
public boolean nextKeyValue() throws IOException, InterruptedException {
    // TODO Auto-generated method stub
    return this.rr.nextKeyValue();
}

@Override
public LongWritable getCurrentKey() throws IOException, InterruptedException {
    // TODO Auto-generated method stub
    return this.rr.getCurrentKey();
}

@Override
public Text getCurrentValue() throws IOException, InterruptedException {
    // TODO Auto-generated method stub
    return this.rr.getCurrentValue();
}

@Override
public float getProgress() throws IOException, InterruptedException {
    // TODO Auto-generated method stub
    return this.rr.getProgress();
}

@Override
public void close() throws IOException {
    if (rr != null) {
           rr.close();
           rr = null;
    }       
}   

}

Answer 1

Take a look into this input format.This is an input format for reading multiple files in a single map task.Exactly one (unsplit) file will be read by each record passed to the mapper. The WholeFileRecordReader takes care of sending one file content as one value. The key returned is NullWritable and value is the content of each file as whole. Now you can use this and run your mapreduce job and see how many mappers actually run and check the output your are getting is correct or not.

Records are constructed from WholeFileRecordReaders.

    public class WholeFileInputFormat extends CombineFileInputFormat<NullWritable, Text>{

        @Override
        protected boolean isSplitable(JobContext context, Path file) {
            return false;
        }

/**
   * Creates a CombineFileRecordReader to read each file assigned to this InputSplit.
   * Note, that unlike ordinary InputSplits, split must be a CombineFileSplit, and therefore
   * is expected to specify multiple files.
   *
   * @param split The InputSplit to read.  Throws an IllegalArgumentException if this is
   *        not a CombineFileSplit.
   * @param context The context for this task.
   * @return a CombineFileRecordReader to process each file in split.
   *         It will read each file with a WholeFileRecordReader.
   * @throws IOException if there is an error.
   */

    @Override
    public RecordReader<NullWritable, Text> createRecordReader(
            InputSplit split, TaskAttemptContext context) throws IOException {

        if (!(split instanceof CombineFileSplit)) {
              throw new IllegalArgumentException("split must be a CombineFileSplit");
            }
            return new CombineFileRecordReader<NullWritable, Text>((CombineFileSplit) split, context, WholeFileRecordReader.class);
    }

    }

Here above you can WholeFileRecordReader is used which is as follows :-

public class WholeFileRecordReader extends RecordReader<NullWritable, Text> {
    private static final Logger LOG = Logger.getLogger(WholeFileRecordReader.class);

      /** The path to the file to read. */
      private final Path mFileToRead;
      /** The length of this file. */
      private final long mFileLength;

      /** The Configuration. */
      private final Configuration mConf;

      /** Whether this FileSplit has been processed. */
      private boolean mProcessed;
      /** Single Text to store the file name of the current file. */
    //  private final Text mFileName;
      /** Single Text to store the value of this file (the value) when it is read. */
      private final Text mFileText;

      /**
       * Implementation detail: This constructor is built to be called via
       * reflection from within CombineFileRecordReader.
       *
       * @param fileSplit The CombineFileSplit that this will read from.
       * @param context The context for this task.
       * @param pathToProcess The path index from the CombineFileSplit to process in this record.
       */
      public WholeFileRecordReader(CombineFileSplit fileSplit, TaskAttemptContext context,
          Integer pathToProcess) {
        mProcessed = false;
        mFileToRead = fileSplit.getPath(pathToProcess);
        mFileLength = fileSplit.getLength(pathToProcess);
        mConf = context.getConfiguration();

        assert 0 == fileSplit.getOffset(pathToProcess);
        if (LOG.isDebugEnabled()) {
          LOG.debug("FileToRead is: " + mFileToRead.toString());
          LOG.debug("Processing path " + pathToProcess + " out of " + fileSplit.getNumPaths());

          try {
            FileSystem fs = FileSystem.get(mConf);
            assert fs.getFileStatus(mFileToRead).getLen() == mFileLength;
          } catch (IOException ioe) {
            // oh well, I was just testing.
          }
        }

    //    mFileName = new Text();
        mFileText = new Text();
      }

      /** {@inheritDoc} */
      @Override
      public void close() throws IOException {
        mFileText.clear();
      }

      /**
       * Returns the absolute path to the current file.
       *
       * @return The absolute path to the current file.
       * @throws IOException never.
       * @throws InterruptedException never.
       */
      @Override
      public NullWritable getCurrentKey() throws IOException, InterruptedException {
        return NullWritable.get();
      }

      /**
       * <p>Returns the current value.  If the file has been read with a call to NextKeyValue(),
       * this returns the contents of the file as a BytesWritable.  Otherwise, it returns an
       * empty BytesWritable.</p>
       *
       * <p>Throws an IllegalStateException if initialize() is not called first.</p>
       *
       * @return A BytesWritable containing the contents of the file to read.
       * @throws IOException never.
       * @throws InterruptedException never.
       */
      @Override
      public Text getCurrentValue() throws IOException, InterruptedException {
        return mFileText;
      }

      /**
       * Returns whether the file has been processed or not.  Since only one record
       * will be generated for a file, progress will be 0.0 if it has not been processed,
       * and 1.0 if it has.
       *
       * @return 0.0 if the file has not been processed.  1.0 if it has.
       * @throws IOException never.
       * @throws InterruptedException never.
       */
      @Override
      public float getProgress() throws IOException, InterruptedException {
        return (mProcessed) ? (float) 1.0 : (float) 0.0;
      }

      /**
       * All of the internal state is already set on instantiation.  This is a no-op.
       *
       * @param split The InputSplit to read.  Unused.
       * @param context The context for this task.  Unused.
       * @throws IOException never.
       * @throws InterruptedException never.
       */
      @Override
      public void initialize(InputSplit split, TaskAttemptContext context)
          throws IOException, InterruptedException {
        // no-op.
      }

      /**
       * <p>If the file has not already been read, this reads it into memory, so that a call
       * to getCurrentValue() will return the entire contents of this file as Text,
       * and getCurrentKey() will return the qualified path to this file as Text.  Then, returns
       * true.  If it has already been read, then returns false without updating any internal state.</p>
       *
       * @return Whether the file was read or not.
       * @throws IOException if there is an error reading the file.
       * @throws InterruptedException if there is an error.
       */
      @Override
      public boolean nextKeyValue() throws IOException, InterruptedException {
        if (!mProcessed) {
          if (mFileLength > (long) Integer.MAX_VALUE) {
            throw new IOException("File is longer than Integer.MAX_VALUE.");
          }
          byte[] contents = new byte[(int) mFileLength];

          FileSystem fs = mFileToRead.getFileSystem(mConf);
          FSDataInputStream in = null;
          try {
            // Set the contents of this file.
            in = fs.open(mFileToRead);
            IOUtils.readFully(in, contents, 0, contents.length);
            mFileText.set(contents, 0, contents.length);

          } finally {
            IOUtils.closeStream(in);
          }
          mProcessed = true;
          return true;
        }
        return false;
      }

}

The following is your driver code:-

public int run(String[] arg) throws Exception {
    Configuration conf=getConf();
    FileSystem fs = FileSystem.get(conf);
    //estimate reducers
    Job job = new Job(conf);
    job.setJarByClass(WholeFileDriver.class);
    job.setJobName("WholeFile");
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(Text.class);
    job.setInputFormatClass(WholeFileInputFormat.class);
    job.setMapperClass(WholeFileMapper.class);
    job.setNumReduceTasks(0);

    FileInputFormat.addInputPath(job, new Path(arg[0]));
    Path output=new Path(arg[1]);
    try {
        fs.delete(output, true);
    } catch (IOException e) {
        LOG.warn("Failed to delete temporary path", e);
    }
    FileOutputFormat.setOutputPath(job, output);

    boolean ret=job.waitForCompletion(true);
    if(!ret){
        throw new Exception("Job Failed");
    }