Example usage for org.apache.hadoop.mapreduce.lib.output FileOutputFormat setOutputPath

Introduction

In this page you can find the example usage for org.apache.hadoop.mapreduce.lib.output FileOutputFormat setOutputPath.

Prototype

public static void setOutputPath(Job job, Path outputDir) 

Source Link

Document

Set the Path of the output directory for the map-reduce job.

Usage

From source file:avro.mr.MapReduceColorCount.java

License:Apache License

public int run(String[] args) throws Exception {
    if (args.length != 2) {
        System.err.println("Usage: MapReduceColorCount <input path> <output path>");
        return -1;
    }/*from ww  w. ja  v  a  2s.  c  o m*/

    Job job = Job.getInstance(getConf());
    job.setJarByClass(MapReduceColorCount.class);
    job.setJobName("Color Count");

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

    job.setInputFormatClass(AvroKeyInputFormat.class);
    job.setMapperClass(ColorCountMapper.class);
    AvroJob.setInputKeySchema(job, User.getClassSchema());
    job.setMapOutputKeyClass(Text.class);
    job.setMapOutputValueClass(IntWritable.class);

    job.setOutputFormatClass(AvroKeyValueOutputFormat.class);
    job.setReducerClass(ColorCountReducer.class);
    AvroJob.setOutputKeySchema(job, Schema.create(Schema.Type.STRING));
    AvroJob.setOutputValueSchema(job, Schema.create(Schema.Type.INT));

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

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From source file:avro.mr.MapReduceColorCountSeqFile.java

License:Apache License

public int run(String[] args) throws Exception {
    if (args.length != 2) {
        System.err.println("Usage: MapReduceColorCount <input path> <output path>");
        return -1;
    }/*  w  w  w .j  a  v  a  2s.  c  om*/

    Job job = Job.getInstance(getConf());
    job.setJarByClass(MapReduceColorCountSeqFile.class);
    job.setJobName("Color Count 2");

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

    job.setInputFormatClass(AvroSequenceFileInputFormat.class);
    AvroJob.setInputKeySchema(job, Schema.create(Schema.Type.LONG));
    AvroJob.setInputValueSchema(job, User.getClassSchema());

    job.setMapperClass(ColorCountMapper.class);
    job.setMapOutputKeyClass(Text.class);
    job.setMapOutputValueClass(IntWritable.class);

    job.setOutputFormatClass(AvroSequenceFileOutputFormat.class);
    job.setReducerClass(ColorCountReducer.class);
    AvroJob.setOutputKeySchema(job, Schema.create(Schema.Type.STRING));
    AvroJob.setOutputValueSchema(job, Schema.create(Schema.Type.INT));

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

---

From source file:basic.PartitionGraph.java

License:Apache License

/**
 * Runs this tool.//from  ww w .  j ava 2 s . c o m
 */
@SuppressWarnings({ "static-access" })
public int run(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(new Option(RANGE, "use range partitioner"));

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("output path").create(OUTPUT));
    options.addOption(
            OptionBuilder.withArgName("num").hasArg().withDescription("number of nodes").create(NUM_NODES));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of partitions")
            .create(NUM_PARTITIONS));

    CommandLine cmdline;
    CommandLineParser parser = new GnuParser();

    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        return -1;
    }

    if (!cmdline.hasOption(INPUT) || !cmdline.hasOption(OUTPUT) || !cmdline.hasOption(NUM_NODES)
            || !cmdline.hasOption(NUM_PARTITIONS)) {
        System.out.println("args: " + Arrays.toString(args));
        HelpFormatter formatter = new HelpFormatter();
        formatter.setWidth(120);
        formatter.printHelp(this.getClass().getName(), options);
        ToolRunner.printGenericCommandUsage(System.out);
        return -1;
    }

    String inPath = cmdline.getOptionValue(INPUT);
    String outPath = cmdline.getOptionValue(OUTPUT);
    int nodeCount = Integer.parseInt(cmdline.getOptionValue(NUM_NODES));
    int numParts = Integer.parseInt(cmdline.getOptionValue(NUM_PARTITIONS));
    boolean useRange = cmdline.hasOption(RANGE);

    LOG.info("Tool name: " + PartitionGraph.class.getSimpleName());
    LOG.info(" - input dir: " + inPath);
    LOG.info(" - output dir: " + outPath);
    LOG.info(" - num partitions: " + numParts);
    LOG.info(" - node cnt: " + nodeCount);
    LOG.info(" - use range partitioner: " + useRange);

    Configuration conf = getConf();
    conf.setInt("NodeCount", nodeCount);

    Job job = Job.getInstance(conf);
    job.setJobName(PartitionGraph.class.getSimpleName() + ":" + inPath);
    job.setJarByClass(PartitionGraph.class);

    job.setNumReduceTasks(numParts);

    FileInputFormat.setInputPaths(job, new Path(inPath));
    FileOutputFormat.setOutputPath(job, new Path(outPath));

    job.setInputFormatClass(NonSplitableSequenceFileInputFormat.class);
    job.setOutputFormatClass(SequenceFileOutputFormat.class);

    job.setMapOutputKeyClass(IntWritable.class);
    job.setMapOutputValueClass(PageRankNode.class);

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

    if (useRange) {
        job.setPartitionerClass(RangePartitioner.class);
    }

    FileSystem.get(conf).delete(new Path(outPath), true);

    job.waitForCompletion(true);

    return 0;
}

---

From source file:bb.BranchAndBound.java

License:Apache License

static Job getJob(String input, String output, String dataDir, int iteration) throws Exception {
    Configuration conf = new Configuration();

    FileSystem hdfs = FileSystem.get(conf);
    FileStatus[] fileStatus = hdfs.listStatus(new Path(input));
    for (int i = 0; i < fileStatus.length; ++i) {
        if (fileStatus[i].getLen() == 0) {
            hdfs.delete(fileStatus[i].getPath());
        }// w ww .  ja  va2  s  .  c  o  m
    }
    DistributedCache.addCacheFile(new URI(dataDir + "/data"), conf);
    Job ret = new Job(conf, dataDir + "_iteration_" + iteration);
    ret.setJarByClass(BranchAndBound.class);
    ret.setMapperClass(BBMapper1.class);
    ret.setReducerClass(BBReducer.class);
    //ret.setReducerClass(MergeReducer.class);
    FileInputFormat.setInputPaths(ret, new Path(input));
    //if( iteration > 7 ) FileInputFormat.setMinInputSplitSize(ret, 67108864);
    FileOutputFormat.setOutputPath(ret, new Path(output));
    ret.setOutputKeyClass(NullWritable.class);
    ret.setOutputValueClass(Text.class);
    return ret;
}

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From source file:bdss.cmu.edu.Sort.java

License:Apache License

/**
 * The main driver for sort program.//from  w w w.  ja  v  a  2s . c  o  m
 * Invoke this method to submit the map/reduce job.
 * @throws IOException When there is communication problems with the
 *                     job tracker.
 */
public int run(String[] args) throws Exception {

    Configuration conf = getConf();
    JobClient client = new JobClient(conf);
    ClusterStatus cluster = client.getClusterStatus();
    int num_reduces = (int) (cluster.getMaxReduceTasks() * 0.9);
    String sort_reduces = conf.get(REDUCES_PER_HOST);
    if (sort_reduces != null) {
        num_reduces = cluster.getTaskTrackers() * Integer.parseInt(sort_reduces);
    }
    Class<? extends InputFormat> inputFormatClass = SequenceFileInputFormat.class;
    Class<? extends OutputFormat> outputFormatClass = SequenceFileOutputFormat.class;
    Class<? extends WritableComparable> outputKeyClass = BytesWritable.class;
    Class<? extends Writable> outputValueClass = BytesWritable.class;
    List<String> otherArgs = new ArrayList<String>();
    InputSampler.Sampler<K, V> sampler = null;
    for (int i = 0; i < args.length; ++i) {
        try {
            if ("-r".equals(args[i])) {
                num_reduces = Integer.parseInt(args[++i]);
            } else if ("-inFormat".equals(args[i])) {
                inputFormatClass = Class.forName(args[++i]).asSubclass(InputFormat.class);
            } else if ("-outFormat".equals(args[i])) {
                outputFormatClass = Class.forName(args[++i]).asSubclass(OutputFormat.class);
            } else if ("-outKey".equals(args[i])) {
                outputKeyClass = Class.forName(args[++i]).asSubclass(WritableComparable.class);
            } else if ("-outValue".equals(args[i])) {
                outputValueClass = Class.forName(args[++i]).asSubclass(Writable.class);
            } else if ("-totalOrder".equals(args[i])) {
                double pcnt = Double.parseDouble(args[++i]);
                int numSamples = Integer.parseInt(args[++i]);
                int maxSplits = Integer.parseInt(args[++i]);
                if (0 >= maxSplits)
                    maxSplits = Integer.MAX_VALUE;
                sampler = new InputSampler.RandomSampler<K, V>(pcnt, numSamples, maxSplits);
            } else {
                otherArgs.add(args[i]);
            }
        } catch (NumberFormatException except) {
            System.out.println("ERROR: Integer expected instead of " + args[i]);
            return printUsage();
        } catch (ArrayIndexOutOfBoundsException except) {
            System.out.println("ERROR: Required parameter missing from " + args[i - 1]);
            return printUsage(); // exits
        }
    }
    // Set user-supplied (possibly default) job configs
    job = new Job(conf);
    job.setJobName("sorter");
    job.setJarByClass(Sort.class);

    job.setMapperClass(Mapper.class);
    job.setReducerClass(Reducer.class);

    job.setNumReduceTasks(num_reduces);

    job.setInputFormatClass(inputFormatClass);
    job.setOutputFormatClass(outputFormatClass);

    job.setOutputKeyClass(outputKeyClass);
    job.setOutputValueClass(outputValueClass);

    // Make sure there are exactly 2 parameters left.
    if (otherArgs.size() != 2) {
        System.out.println("ERROR: Wrong number of parameters: " + otherArgs.size() + " instead of 2.");
        return printUsage();
    }
    FileInputFormat.setInputPaths(job, otherArgs.get(0));
    FileOutputFormat.setOutputPath(job, new Path(otherArgs.get(1)));

    if (sampler != null) {
        System.out.println("Sampling input to effect total-order sort...");
        job.setPartitionerClass(TotalOrderPartitioner.class);
        Path inputDir = FileInputFormat.getInputPaths(job)[0];
        inputDir = inputDir.makeQualified(inputDir.getFileSystem(conf));
        Path partitionFile = new Path(inputDir, "_sortPartitioning");
        TotalOrderPartitioner.setPartitionFile(job.getConfiguration(), partitionFile);
        InputSampler.<K, V>writePartitionFile(job, sampler);
        URI partitionUri = new URI(partitionFile.toString() + "#" + "_sortPartitioning");
        DistributedCache.addCacheFile(partitionUri, conf);
    }

    System.out.println("Running on " + cluster.getTaskTrackers() + " nodes to sort from "
            + FileInputFormat.getInputPaths(job)[0] + " into " + FileOutputFormat.getOutputPath(job) + " with "
            + num_reduces + " reduces.");
    Date startTime = new Date();
    System.out.println("Job started: " + startTime);
    int ret = job.waitForCompletion(true) ? 0 : 1;
    Date end_time = new Date();
    System.out.println("Job ended: " + end_time);
    System.out.println("The job took " + (end_time.getTime() - startTime.getTime()) / 1000 + " seconds.");
    return ret;
}

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From source file:be.ugent.intec.halvade.MapReduceRunner.java

License:Open Source License

protected int runPass1RNAJob(Configuration pass1Conf, String tmpOutDir)
        throws IOException, InterruptedException, ClassNotFoundException, URISyntaxException {
    HalvadeConf.setIsPass2(pass1Conf, false);
    HalvadeResourceManager.setJobResources(halvadeOpts, pass1Conf, HalvadeResourceManager.RNA_SHMEM_PASS1, true,
            halvadeOpts.useBamInput);//from w  w w . j a v  a2  s  .  co m
    Job pass1Job = Job.getInstance(pass1Conf, "Halvade pass 1 RNA pipeline");
    pass1Job.addCacheArchive(new URI(halvadeOpts.halvadeBinaries));
    pass1Job.setJarByClass(be.ugent.intec.halvade.hadoop.mapreduce.HalvadeMapper.class);
    FileSystem fs = FileSystem.get(new URI(halvadeOpts.in), pass1Conf);
    try {
        if (fs.getFileStatus(new Path(halvadeOpts.in)).isDirectory()) {
            // add every file in directory
            FileStatus[] files = fs.listStatus(new Path(halvadeOpts.in));
            for (FileStatus file : files) {
                if (!file.isDirectory()) {
                    FileInputFormat.addInputPath(pass1Job, file.getPath());
                }
            }
        } else {
            FileInputFormat.addInputPath(pass1Job, new Path(halvadeOpts.in));
        }
    } catch (IOException | IllegalArgumentException e) {
        Logger.EXCEPTION(e);
    }

    FileSystem outFs = FileSystem.get(new URI(tmpOutDir), pass1Conf);
    boolean skipPass1 = false;
    if (outFs.exists(new Path(tmpOutDir))) {
        // check if genome already exists
        skipPass1 = outFs.exists(new Path(tmpOutDir + "/_SUCCESS"));
        if (skipPass1)
            Logger.DEBUG("pass1 genome already created, skipping pass 1");
        else {
            Logger.INFO("The output directory \'" + tmpOutDir + "\' already exists.");
            Logger.INFO("ERROR: Please remove this directory before trying again.");
            System.exit(-2);
        }
    }
    if (!skipPass1) {
        FileOutputFormat.setOutputPath(pass1Job, new Path(tmpOutDir));
        pass1Job.setMapperClass(be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.class);

        pass1Job.setInputFormatClass(HalvadeTextInputFormat.class);
        pass1Job.setMapOutputKeyClass(GenomeSJ.class);
        pass1Job.setMapOutputValueClass(Text.class);

        pass1Job.setSortComparatorClass(GenomeSJSortComparator.class);
        pass1Job.setGroupingComparatorClass(GenomeSJGroupingComparator.class);
        pass1Job.setNumReduceTasks(1);
        pass1Job.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.RebuildStarGenomeReducer.class);
        pass1Job.setOutputKeyClass(LongWritable.class);
        pass1Job.setOutputValueClass(Text.class);

        return runTimedJob(pass1Job, "Halvade pass 1 Job");
    } else
        return 0;
}

---

From source file:be.ugent.intec.halvade.MapReduceRunner.java

License:Open Source License

protected int runHalvadeJob(Configuration halvadeConf, String tmpOutDir, int jobType)
        throws IOException, URISyntaxException, InterruptedException, ClassNotFoundException {
    String pipeline = "";
    if (jobType == HalvadeResourceManager.RNA_SHMEM_PASS2) {
        HalvadeConf.setIsPass2(halvadeConf, true);
        HalvadeResourceManager.setJobResources(halvadeOpts, halvadeConf, jobType, false,
                halvadeOpts.useBamInput);
        pipeline = RNA_PASS2;//  ww  w .  ja v  a  2 s  .c  o  m
    } else if (jobType == HalvadeResourceManager.DNA) {
        HalvadeResourceManager.setJobResources(halvadeOpts, halvadeConf, jobType, false,
                halvadeOpts.useBamInput);
        pipeline = DNA;
    }
    HalvadeConf.setOutDir(halvadeConf, tmpOutDir);
    FileSystem outFs = FileSystem.get(new URI(tmpOutDir), halvadeConf);
    if (outFs.exists(new Path(tmpOutDir))) {
        Logger.INFO("The output directory \'" + tmpOutDir + "\' already exists.");
        Logger.INFO("ERROR: Please remove this directory before trying again.");
        System.exit(-2);
    }
    if (halvadeOpts.useBamInput)
        setHeaderFile(halvadeOpts.in, halvadeConf);

    Job halvadeJob = Job.getInstance(halvadeConf, "Halvade" + pipeline);
    halvadeJob.addCacheArchive(new URI(halvadeOpts.halvadeBinaries));
    halvadeJob.setJarByClass(be.ugent.intec.halvade.hadoop.mapreduce.HalvadeMapper.class);
    addInputFiles(halvadeOpts.in, halvadeConf, halvadeJob);
    FileOutputFormat.setOutputPath(halvadeJob, new Path(tmpOutDir));

    if (jobType == HalvadeResourceManager.RNA_SHMEM_PASS2) {
        halvadeJob.setMapperClass(be.ugent.intec.halvade.hadoop.mapreduce.StarAlignPassXMapper.class);
        halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.RnaGATKReducer.class);
    } else if (jobType == HalvadeResourceManager.DNA) {
        halvadeJob.setMapperClass(halvadeOpts.alignmentTools[halvadeOpts.aln]);
        halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.DnaGATKReducer.class);
    }

    halvadeJob.setMapOutputKeyClass(ChromosomeRegion.class);
    halvadeJob.setMapOutputValueClass(SAMRecordWritable.class);
    halvadeJob.setInputFormatClass(HalvadeTextInputFormat.class);
    halvadeJob.setOutputKeyClass(Text.class);
    if (halvadeOpts.mergeBam) {
        halvadeJob.setSortComparatorClass(SimpleChrRegionComparator.class);
        halvadeJob.setOutputValueClass(SAMRecordWritable.class);
    } else {
        halvadeJob.setPartitionerClass(ChrRgPartitioner.class);
        halvadeJob.setSortComparatorClass(ChrRgSortComparator.class);
        halvadeJob.setGroupingComparatorClass(ChrRgGroupingComparator.class);
        halvadeJob.setOutputValueClass(VariantContextWritable.class);
    }

    if (halvadeOpts.justAlign)
        halvadeJob.setNumReduceTasks(0);
    else if (halvadeOpts.mergeBam) {
        halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.BamMergeReducer.class);
        halvadeJob.setNumReduceTasks(1);
    } else
        halvadeJob.setNumReduceTasks(halvadeOpts.reduces);

    if (halvadeOpts.useBamInput) {
        halvadeJob.setMapperClass(be.ugent.intec.halvade.hadoop.mapreduce.AlignedBamMapper.class);
        halvadeJob.setInputFormatClass(BAMInputFormat.class);
    }

    return runTimedJob(halvadeJob, "Halvade Job");
}

---

From source file:be.ugent.intec.halvade.MapReduceRunner.java

License:Open Source License

protected int runCombineJob(String halvadeOutDir, String mergeOutDir, boolean featureCount)
        throws IOException, URISyntaxException, InterruptedException, ClassNotFoundException {
    Configuration combineConf = getConf();
    if (!halvadeOpts.out.endsWith("/"))
        halvadeOpts.out += "/";
    HalvadeConf.setInputDir(combineConf, halvadeOutDir);
    HalvadeConf.setOutDir(combineConf, mergeOutDir);
    FileSystem outFs = FileSystem.get(new URI(mergeOutDir), combineConf);
    if (outFs.exists(new Path(mergeOutDir))) {
        Logger.INFO("The output directory \'" + mergeOutDir + "\' already exists.");
        Logger.INFO("ERROR: Please remove this directory before trying again.");
        System.exit(-2);//from w w  w  .j  av  a 2  s  .  c o m
    }
    HalvadeConf.setReportAllVariant(combineConf, halvadeOpts.reportAll);
    HalvadeResourceManager.setJobResources(halvadeOpts, combineConf, HalvadeResourceManager.COMBINE, false,
            halvadeOpts.useBamInput);
    Job combineJob = Job.getInstance(combineConf, "HalvadeCombineVCF");
    combineJob.setJarByClass(be.ugent.intec.halvade.hadoop.mapreduce.VCFCombineMapper.class);

    addInputFiles(halvadeOutDir, combineConf, combineJob, featureCount ? ".count" : ".vcf");
    FileOutputFormat.setOutputPath(combineJob, new Path(mergeOutDir));

    combineJob.setMapperClass(featureCount ? be.ugent.intec.halvade.hadoop.mapreduce.HTSeqCombineMapper.class
            : be.ugent.intec.halvade.hadoop.mapreduce.VCFCombineMapper.class);
    combineJob.setMapOutputKeyClass(featureCount ? Text.class : LongWritable.class);
    combineJob.setMapOutputValueClass(featureCount ? LongWritable.class : VariantContextWritable.class);
    combineJob.setInputFormatClass(featureCount ? TextInputFormat.class : VCFInputFormat.class);
    combineJob.setNumReduceTasks(1);
    combineJob.setReducerClass(featureCount ? be.ugent.intec.halvade.hadoop.mapreduce.HTSeqCombineReducer.class
            : be.ugent.intec.halvade.hadoop.mapreduce.VCFCombineReducer.class);
    combineJob.setOutputKeyClass(Text.class);
    combineJob.setOutputValueClass(featureCount ? LongWritable.class : VariantContextWritable.class);

    return runTimedJob(combineJob, (featureCount ? "featureCounts" : "VCF") + " Combine Job");
}

---

From source file:be_uclouvain_ingi2145_lab05.GiraphJobRunner.java

@Override
public int run(String[] strings) throws Exception {

    GiraphConfiguration gconf = new GiraphConfiguration(conf);
    //gconf.setVertexClass(SimpleShortestPathsComputation.class);
    /*gconf.setVertexInputFormatClass(
        SimpleShortestPathsVertexInputFormat.class);
    gconf.setVertexOutputFormatClass(/*w  w w .j a va2 s  . co m*/
        SimpleShortestPathsVertexOutputFormat.class);
    */
    CommandLine cmd = ConfigurationUtils.parseArgs(gconf, strings);
    if (null == cmd) {
        return 0;
    }

    //GiraphYarnClient job = new GiraphYarnClient(gconf,gconf.getClass().getName());
    GiraphJob job = new GiraphJob(gconf, getClass().getName());
    job.getInternalJob().setJarByClass(getClass());
    if (cmd.hasOption("vof") || cmd.hasOption("eof")) {
        if (cmd.hasOption("op")) {
            Path outputPath = new Path(cmd.getOptionValue("op"));

            FileSystem fs = FileSystem.get(outputPath.toUri(), conf);
            /*Check if output path (args[1])exist or not*/
            if (fs.exists(outputPath)) {
                /*If exist delete the output path*/
                fs.delete(outputPath, true);
            }

            FileOutputFormat.setOutputPath(job.getInternalJob(), outputPath);
        }
    }
    /*
    if (cmd.hasOption("vif") || cmd.hasOption("eif")) {
      if (cmd.hasOption("vip")) {
          FileInputFormat.addInputPath(job.getInternalJob(), new Path(cmd.getOptionValue("op")));
      }
    }*/
    //If there is a custom option specified
    if (cmd.hasOption("ca")) {
        String[] args = cmd.getOptionValues("ca");
        LOG.fatal("" + Arrays.toString(args));

        gconf.set("ca", args[0].split("=")[1]);
        LOG.fatal("" + gconf.get("ca"));
        gconf.setWorkerConfiguration(Integer.parseInt(cmd.getOptionValue("w")),
                Integer.parseInt(cmd.getOptionValue("w")), 100.0f);
    }
    /*
    if (cmd.hasOption("cf")) {
      DistributedCache.addCacheFile(new URI(cmd.getOptionValue("cf")),
          job.getConfiguration());
    }
    */
    return job.run(true) ? 0 : -1;
}

---

From source file:biglayer.AutoCoder.java

License:Apache License

/**
 * Runs this tool./*from   w  ww  .j a va2  s.c om*/
 */
@SuppressWarnings({ "static-access" })
public int run(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("input path").create(INPUT));
    options.addOption(OptionBuilder.withArgName("path").hasArg().withDescription("output path").create(OUTPUT));
    options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of reducers")
            .create(NUM_REDUCERS));

    CommandLine cmdline;
    CommandLineParser parser = new GnuParser();

    try {
        cmdline = parser.parse(options, args);
    } catch (ParseException exp) {
        System.err.println("Error parsing command line: " + exp.getMessage());
        return -1;
    }

    /*if (!cmdline.hasOption(INPUT) || !cmdline.hasOption(OUTPUT)) {
       System.out.println("args: " + Arrays.toString(args));
       HelpFormatter formatter = new HelpFormatter();
       formatter.setWidth(120);
       formatter.printHelp(this.getClass().getName(), options);
       ToolRunner.printGenericCommandUsage(System.out);
       return -1;
    }*/

    //String inputPath = cmdline.getOptionValue(INPUT);
    //String outputPath = cmdline.getOptionValue(OUTPUT);

    String inputPath = "qiwang321/MNIST-mingled-key/part*";
    String outputPath = "shangfu/layeroutput";

    int reduceTasks = cmdline.hasOption(NUM_REDUCERS) ? Integer.parseInt(cmdline.getOptionValue(NUM_REDUCERS))
            : 1;

    LOG.info("Tool: " + AutoCoder.class.getSimpleName());
    LOG.info(" - input path: " + inputPath);
    LOG.info(" - output path: " + outputPath);
    LOG.info(" - number of reducers: " + reduceTasks);
    Configuration conf = getConf();

    conf.setInt("num_reduce_task", reduceTasks);
    conf.set("sidepath", outputPath + "_side/");

    Job job0 = Job.getInstance(conf);
    job0.setJobName(AutoCoder.class.getSimpleName());
    job0.setJarByClass(AutoCoder.class);
    job0.setNumReduceTasks(reduceTasks);

    job0.getConfiguration().setInt("layer_ind", 0);

    FileInputFormat.setInputPaths(job0, new Path(inputPath));
    FileOutputFormat.setOutputPath(job0, new Path(outputPath + "_0"));

    job0.setInputFormatClass(KeyValueTextInputFormat.class);
    job0.setOutputFormatClass(SequenceFileOutputFormat.class);

    job0.setMapOutputKeyClass(PairOfInts.class);
    job0.setMapOutputValueClass(ModelNode.class);
    job0.setOutputKeyClass(PairOfInts.class);
    job0.setOutputValueClass(ModelNode.class);

    job0.setMapperClass(MyMapper0.class);
    job0.setReducerClass(MyReducer0.class);
    job0.setPartitionerClass(MyPartitioner.class);
    // Delete the output directory if it exists already.
    Path outputDir = new Path(outputPath + "_0");
    FileSystem.get(getConf()).delete(outputDir, true);
    long startTime = System.currentTimeMillis();
    long codeStart = System.currentTimeMillis();
    double codeTimeSum = 0;
    job0.waitForCompletion(true);
    LOG.info("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");
    codeTimeSum += (System.currentTimeMillis() - startTime) / 1000.0;

    for (int iterations = 1; iterations < GlobalUtil.NUM_LAYER + 1; iterations++) {
        Job job1 = Job.getInstance(conf);
        job1.setJobName(AutoCoder.class.getSimpleName());
        job1.setJarByClass(AutoCoder.class);
        job1.setNumReduceTasks(reduceTasks);
        job1.getConfiguration().setInt("layer_ind", iterations);
        FileInputFormat.setInputPaths(job1, new Path(outputPath + "_" + (iterations - 1)));
        FileOutputFormat.setOutputPath(job1, new Path(outputPath + "_" + iterations + "_train"));

        LOG.info("Tool: " + AutoCoder.class.getSimpleName());
        LOG.info(" - input path: " + outputPath + "_" + (iterations - 1));
        LOG.info(" - output path: " + outputPath + "_" + iterations + "_train");
        LOG.info(" - number of reducers: " + reduceTasks);

        job1.setInputFormatClass(SequenceFileInputFormat.class);
        job1.setOutputFormatClass(SequenceFileOutputFormat.class);

        job1.setMapOutputKeyClass(PairOfInts.class);
        job1.setMapOutputValueClass(ModelNode.class);
        job1.setOutputKeyClass(PairOfInts.class);
        job1.setOutputValueClass(ModelNode.class);

        job1.setMapperClass(MyMapper.class);
        job1.setReducerClass(MyReducer_Train.class);
        job1.setPartitionerClass(MyPartitioner.class);
        // Delete the output directory if it exists already.
        outputDir = new Path(outputPath + "_" + iterations + "_train");
        FileSystem.get(getConf()).delete(outputDir, true);
        startTime = System.currentTimeMillis();
        job1.waitForCompletion(true);
        LOG.info("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");
        codeTimeSum += (System.currentTimeMillis() - startTime) / 1000.0;

        Job job2 = Job.getInstance(conf);
        job2.setJobName(AutoCoder.class.getSimpleName());
        job2.setJarByClass(AutoCoder.class);
        job2.setNumReduceTasks(reduceTasks);
        job2.getConfiguration().setInt("layer_ind", iterations);
        FileInputFormat.setInputPaths(job2, new Path(outputPath + "_" + (iterations + "_train")));
        FileOutputFormat.setOutputPath(job2, new Path(outputPath + "_" + iterations));

        LOG.info("Tool: " + AutoCoder.class.getSimpleName());
        LOG.info(" - input path: " + outputPath + "_" + iterations + "_train");
        LOG.info(" - output path: " + outputPath + "_" + iterations);
        LOG.info(" - number of reducers: " + reduceTasks);

        job2.setInputFormatClass(SequenceFileInputFormat.class);
        job2.setOutputFormatClass(SequenceFileOutputFormat.class);

        job2.setMapOutputKeyClass(PairOfInts.class);
        job2.setMapOutputValueClass(ModelNode.class);
        job2.setOutputKeyClass(PairOfInts.class);
        job2.setOutputValueClass(ModelNode.class);

        job2.setMapperClass(MyMapper.class);
        job2.setReducerClass(MyReducer_GenData.class);
        job2.setPartitionerClass(MyPartitioner.class);
        // Delete the output directory if it exists already.
        outputDir = new Path(outputPath + "_" + iterations);
        FileSystem.get(getConf()).delete(outputDir, true);
        startTime = System.currentTimeMillis();
        job2.waitForCompletion(true);
        LOG.info("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");
        codeTimeSum += (System.currentTimeMillis() - startTime) / 1000.0;

    }

    LOG.info(" - input path: " + outputPath + "_" + GlobalUtil.NUM_LAYER);
    LOG.info(" - output path: " + outputPath);
    reduceTasks = 1;
    LOG.info(" - number of reducers: " + reduceTasks);

    Job job_super = Job.getInstance(conf);
    job_super.setJobName(AutoCoder.class.getSimpleName());
    job_super.setJarByClass(AutoCoder.class);
    job_super.setNumReduceTasks(reduceTasks);

    FileInputFormat.setInputPaths(job_super, new Path(outputPath + "_" + GlobalUtil.NUM_LAYER));
    FileOutputFormat.setOutputPath(job_super, new Path(outputPath));

    job_super.setInputFormatClass(SequenceFileInputFormat.class);
    job_super.setOutputFormatClass(SequenceFileOutputFormat.class);

    job_super.setMapOutputKeyClass(PairOfInts.class);
    job_super.setMapOutputValueClass(ModelNode.class);
    job_super.setOutputKeyClass(NullWritable.class);
    job_super.setOutputValueClass(NullWritable.class);

    job_super.setMapperClass(MyMapper_Super.class);
    job_super.setReducerClass(MyReducer_Super.class);
    job_super.setPartitionerClass(MyPartitioner.class);

    // Delete the output directory if it exists already.
    outputDir = new Path(outputPath);
    FileSystem.get(getConf()).delete(outputDir, true);

    startTime = System.currentTimeMillis();
    job_super.waitForCompletion(true);
    LOG.info("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");
    codeTimeSum += (System.currentTimeMillis() - startTime) / 1000.0;

    Log.info("Final Time: " + ((System.currentTimeMillis() - codeStart) / 1000.0) + " seconds,  " + codeTimeSum
            + " seconds.");
    //prepareNextIteration(inputPath0, outputPath,iterations,conf,reduceTasks);

    return 0;
}

---

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