Example usage for org.apache.hadoop.mapreduce Job setMapOutputKeyClass

Introduction

In this page you can find the example usage for org.apache.hadoop.mapreduce Job setMapOutputKeyClass.

Prototype

public void setMapOutputKeyClass(Class<?> theClass) throws IllegalStateException 

Source Link

Document

Set the key class for the map output data.

Usage

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  .  jav a 2 s  . c o 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.  j a v  a 2  s  .co  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  www.  j a v 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:biglayer.AutoCoder.java

License:Apache License

/**
 * Runs this tool.//from   w w w . j  a  va2s . co  m
 */
@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;
}

---

From source file:bigmodel.AutoCoderLocal.java

License:Apache License

/**
 * Runs this tool./*from ww w.ja va  2 s .c  o  m*/
 */
@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) + "/part-r-00000";
    String outputPath = cmdline.getOptionValue(OUTPUT);
    String dataPath = cmdline.getOptionValue(INPUT) + "/common";
    //String inputPath = "/home/qiwang321/mapreduce-data/data/in-mingled1-5/part*";
    //String outputPath = "output";
    //String dataPath = "/home/qiwang321/mapreduce-data/data/in-mingled1-5/common";
    int reduceTasks = cmdline.hasOption(NUM_REDUCERS) ? Integer.parseInt(cmdline.getOptionValue(NUM_REDUCERS))
            : 1;

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

    conf.set("dataPath", dataPath);

    Job job = Job.getInstance(conf);
    job.setJobName(AutoCoderLocal.class.getSimpleName());
    job.setJarByClass(AutoCoderLocal.class);
    // set the path of the information of k clusters in this iteration
    job.getConfiguration().set("sidepath", inputPath + "/side_output");
    job.setNumReduceTasks(reduceTasks);

    dataShuffle();

    FileInputFormat.setInputPaths(job, new Path(inputPath));
    FileOutputFormat.setOutputPath(job, new Path(outputPath));
    FileInputFormat.setMinInputSplitSize(job, 1000 * 1024 * 1024);
    FileInputFormat.setMaxInputSplitSize(job, 1000 * 1024 * 1024);

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

    job.setMapOutputKeyClass(IntWritable.class);
    job.setMapOutputValueClass(ModelNode.class);
    job.setOutputKeyClass(NullWritable.class);
    job.setOutputValueClass(SuperModel.class);

    job.setMapperClass(MyMapper.class);
    job.setReducerClass(MyReducer.class);
    job.setPartitionerClass(MyPartitioner.class);

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

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

    //prepareNextIteration(inputPath0, outputPath,iterations,conf,reduceTasks);

    return 0;
}

---

From source file:bigsidemodel.AutoCoder.java

License:Apache License

/**
 * Runs this tool.//w w w.  j  a v  a2 s. c o  m
 */
@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/best5-mingled-key-56x56/part*";
    String outputPath = "shangfu/bigoutput";
    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 + "0");
    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);
    // set the path of the information of k clusters in this iteration
    job0.setNumReduceTasks(reduceTasks);

    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(DataNode.class);
    job0.setOutputKeyClass(PairOfInts.class);
    job0.setOutputValueClass(DataNode.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 codeStart = System.currentTimeMillis();
    double jobTimeSum = 0;

    long startTime = System.currentTimeMillis();
    job0.waitForCompletion(true);
    LOG.info("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");
    jobTimeSum += (System.currentTimeMillis() - startTime) / 1000.0;

    //======= Job 1
    LOG.info("Tool: " + AutoCoder.class.getSimpleName());
    LOG.info(" - input path: " + outputPath + "0");
    LOG.info(" - output path: " + outputPath + "1");
    LOG.info(" - number of reducers: " + 1);
    int nModel = reduceTasks;
    reduceTasks = 1;

    Job job1 = Job.getInstance(conf);
    job1.setJobName(AutoCoder.class.getSimpleName());
    job1.setJarByClass(AutoCoder.class);
    // set the path of the information of k clusters in this iteration
    job1.setNumReduceTasks(reduceTasks);

    FileInputFormat.setInputPaths(job1, new Path(outputPath + "0"));
    FileOutputFormat.setOutputPath(job1, new Path(outputPath + "1"));

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

    job1.setMapOutputKeyClass(PairOfInts.class);
    job1.setMapOutputValueClass(DataNode.class);
    job1.setOutputKeyClass(NullWritable.class);
    job1.setOutputValueClass(NullWritable.class);

    job1.setMapperClass(MyMapper1.class);
    job1.setReducerClass(MyReducer1.class);
    job1.setPartitionerClass(MyPartitioner.class);

    // Delete the output directory if it exists already.
    outputDir = new Path(outputPath + "1");
    FileSystem.get(getConf()).delete(outputDir, true);

    startTime = System.currentTimeMillis();
    job1.waitForCompletion(true);
    LOG.info("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");
    jobTimeSum += (System.currentTimeMillis() - startTime) / 1000.0;
    LOG.info("Final Time: " + ((System.currentTimeMillis() - codeStart) / 1000.0) + " seconds,  " + jobTimeSum
            + " seconds.");

    return 0;
}

---

From source file:BinningByState.Driver.java

public static void main(String args[]) throws IOException, InterruptedException, ClassNotFoundException {
    Configuration conf = new Configuration();
    Job job = Job.getInstance(conf, "BinningByState");
    MultipleOutputs.addNamedOutput(job, "bins", TextOutputFormat.class, Text.class, NullWritable.class);
    MultipleOutputs.setCountersEnabled(job, true);
    job.setJarByClass(Driver.class);
    job.setMapperClass(BinningMapper.class);
    job.setMapOutputKeyClass(Text.class);
    job.setMapOutputValueClass(NullWritable.class);
    job.setNumReduceTasks(0);/*from w  w  w . j a  v  a  2 s. c o m*/
    //        job.setOutputKeyClass(Text.class);
    //        job.setOutputValueClass(NullWritable.class);
    FileInputFormat.addInputPath(job, new Path(args[0]));
    FileOutputFormat.setOutputPath(job, new Path(args[1]));

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

---

From source file:boa.runtime.BoaRunner.java

License:Apache License

/**
 * Create a {@link Job} describing the work to be done by this Boa job.
 * //from  w  ww  .  j a  va2s.  com
 * @param ins
 *            An array of {@link Path} containing the locations of the input
 *            files
 * 
 * @param out
 *            A {@link Path} containing the location of the output file
 * 
 * @param robust
 *            A boolean representing whether the job should ignore most
 *            exceptions
 * 
 * @return A {@link Job} describing the work to be done by this Boa job
 * @throws IOException
 */
public Job job(final Path[] ins, final Path out, final boolean robust) throws IOException {
    final Configuration configuration = getConf();

    configuration.setBoolean("boa.runtime.robust", robust);

    // faster local reads
    configuration.setBoolean("dfs.client.read.shortcircuit", true);
    configuration.setBoolean("dfs.client.read.shortcircuit.skip.checksum", true);

    // by default our MapFile's index every key, which takes up
    // a lot of memory - this lets you skip keys in the index and
    // control the memory requirements (as a tradeoff of slower gets)
    //configuration.setLong("io.map.index.skip", 128);

    // map output compression
    configuration.setBoolean("mapred.compress.map.output", true);
    configuration.set("mapred.map.output.compression.type", "BLOCK");
    configuration.setClass("mapred.map.output.compression.codec", SnappyCodec.class, CompressionCodec.class);

    configuration.setBoolean("mapred.map.tasks.speculative.execution", false);
    configuration.setBoolean("mapred.reduce.tasks.speculative.execution", false);
    configuration.setLong("mapred.job.reuse.jvm.num.tasks", -1);

    final Job job = new Job(configuration);

    if (ins != null)
        for (final Path in : ins)
            FileInputFormat.addInputPath(job, in);
    FileOutputFormat.setOutputPath(job, out);

    job.setPartitionerClass(BoaPartitioner.class);

    job.setMapOutputKeyClass(EmitKey.class);
    job.setMapOutputValueClass(EmitValue.class);

    job.setOutputFormatClass(BoaOutputFormat.class);
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(NullWritable.class);

    return job;
}

---

From source file:boostingPL.driver.AdaBoostPLDriver.java

License:Open Source License

@Override
public int run(String[] args) throws Exception {
    int status = commandAnalysis(args);
    if (status != 0) {
        return status;
    }/*  w w  w. j  a v  a  2s  .  c o m*/

    @SuppressWarnings("deprecation")
    Job job = new Job(getConf());
    job.setJobName("AdaBoostPL:" + runModel + " " + dataPath.toString() + " " + modelPath.toString() + " "
            + numLinesPerMap + " " + numIterations);
    job.setJarByClass(AdaBoostPLDriver.class);

    job.setInputFormatClass(NLineInputFormat.class);
    NLineInputFormat.addInputPath(job, dataPath);
    NLineInputFormat.setNumLinesPerSplit(job, numLinesPerMap);

    if (runModel.equals("train")) {
        job.setMapperClass(AdaBoostPLMapper.class);

        job.setMapOutputKeyClass(IntWritable.class);
        job.setMapOutputValueClass(ClassifierWritable.class);
        job.setOutputKeyClass(IntWritable.class);
        job.setOutputValueClass(ClassifierWritable.class);

        job.setOutputFormatClass(SequenceFileOutputFormat.class);
        SequenceFileOutputFormat.setOutputPath(job, modelPath);
    } else {
        job.setMapperClass(AdaBoostPLTestMapper.class);
        job.setReducerClass(AdaBoostPLTestReducer.class);
        job.setOutputFormatClass(NullOutputFormat.class);

        job.setMapOutputKeyClass(LongWritable.class);
        job.setMapOutputValueClass(Text.class);
        job.setOutputKeyClass(NullWritable.class);
        job.setOutputValueClass(NullWritable.class);
    }

    Configuration conf = job.getConfiguration();
    conf.set("BoostingPL.boostingName", "AdaBoost");
    conf.set("BoostingPL.numIterations", String.valueOf(numIterations));
    conf.set("BoostingPL.modelPath", modelPath.toString());
    if (metadataPath == null) {
        conf.set("BoostingPL.metadata", dataPath.toString() + ".metadata");
    } else {
        conf.set("BoostingPL.metadata", metadataPath.toString());
    }
    if (outputFolder != null) {
        conf.set("BoostingPL.outputFolder", outputFolder.toString());
    }

    LOG.info(StringUtils.arrayToString(args));
    return job.waitForCompletion(true) == true ? 0 : -1;
}

---

From source file:boostingPL.driver.SAMMEPLDriver.java

License:Open Source License

@Override
public int run(String[] args) throws Exception {
    int status = commandAnalysis(args);
    if (status != 0) {
        return status;
    }/*  www  .  java2s .  c om*/

    @SuppressWarnings("deprecation")
    Job job = new Job(getConf());
    job.setJobName("SAMMEPL:" + runModel + " " + dataPath.toString() + " " + modelPath.toString() + " "
            + numLinesPerMap + " " + numIterations);
    job.setJarByClass(SAMMEPLDriver.class);

    job.setInputFormatClass(NLineInputFormat.class);
    NLineInputFormat.addInputPath(job, dataPath);
    NLineInputFormat.setNumLinesPerSplit(job, numLinesPerMap);
    FileSystem fs = modelPath.getFileSystem(getConf());
    if (fs.exists(modelPath)) {
        fs.delete(modelPath, true);
    }
    job.setOutputFormatClass(SequenceFileOutputFormat.class);
    SequenceFileOutputFormat.setOutputPath(job, modelPath);

    if (runModel.equals("train")) {
        job.setMapperClass(AdaBoostPLMapper.class);

        job.setMapOutputKeyClass(IntWritable.class);
        job.setMapOutputValueClass(ClassifierWritable.class);
        job.setOutputKeyClass(IntWritable.class);
        job.setOutputValueClass(ClassifierWritable.class);
    } else {
        job.setMapperClass(AdaBoostPLTestMapper.class);
        job.setReducerClass(AdaBoostPLTestReducer.class);
        job.setOutputFormatClass(NullOutputFormat.class);

        job.setMapOutputKeyClass(LongWritable.class);
        job.setMapOutputValueClass(Text.class);
        job.setOutputKeyClass(NullWritable.class);
        job.setOutputValueClass(NullWritable.class);
    }

    Configuration conf = job.getConfiguration();
    conf.set("BoostingPL.boostingName", "SAMME");
    conf.set("BoostingPL.numIterations", String.valueOf(numIterations));
    conf.set("BoostingPL.modelPath", modelPath.toString());
    if (metadataPath == null) {
        conf.set("BoostingPL.metadata", dataPath.toString() + ".metadata");
    } else {
        conf.set("BoostingPL.metadata", metadataPath.toString());
    }
    if (outputFolder != null) {
        conf.set("BoostingPL.outputFolder", outputFolder.toString());
    }

    LOG.info(StringUtils.arrayToString(args));
    return job.waitForCompletion(true) == true ? 0 : -1;
}

---

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