List of usage examples for org.apache.hadoop.mapreduce Job setGroupingComparatorClass
public void setGroupingComparatorClass(Class<? extends RawComparator> cls) throws IllegalStateException
From source file:DescSorter.java
License:Apache License
public static void main(String[] args) throws Exception { Configuration conf = new Configuration(); String[] otherArgs = new GenericOptionsParser(conf, args).getRemainingArgs(); if (otherArgs.length < 2) { System.err.println("Usage: flights <in> <in> <out>"); System.exit(2);// w w w .j a v a 2 s. c o m } Job job = new Job(conf, "AvgDelays"); job.setJarByClass(DescSorter.class); job.setMapperClass(FlightMapper.class); job.setMapOutputKeyClass(CompositeKey.class); job.setMapOutputValueClass(IntWritable.class); job.setPartitionerClass(CompositeKeyPartitioner.class); job.setSortComparatorClass(SortComparator.class); job.setGroupingComparatorClass(GroupingComparator.class); job.setReducerClass(AvgDelayReducer.class); job.setOutputKeyClass(IntWritable.class); job.setOutputValueClass(Text.class); for (int i = 0; i < otherArgs.length - 1; ++i) { FileInputFormat.addInputPath(job, new Path(otherArgs[i])); } FileOutputFormat.setOutputPath(job, new Path(otherArgs[otherArgs.length - 1])); System.exit(job.waitForCompletion(true) ? 0 : 1); }
From source file:AllLab_Skeleton.Lab2.Lab2SecondarySort.java
/** * @param args the command line arguments *///w ww . java 2 s .co m public static void main(String[] args) { try { Configuration conf = new Configuration(); Job job = Job.getInstance(conf, "SecondarySort"); job.setJarByClass(Lab2SecondarySort.class); job.setMapperClass(Lab2Mapper.class); job.setMapOutputKeyClass(CompositeKeyWritable.class); job.setMapOutputValueClass(NullWritable.class); job.setPartitionerClass(Lab2Partitioner.class); job.setGroupingComparatorClass(Lab2GroupComparator.class); job.setReducerClass(Lab2Reducer.class); job.setOutputKeyClass(CompositeKeyWritable.class); job.setOutputValueClass(NullWritable.class); job.setNumReduceTasks(8); FileInputFormat.addInputPath(job, new Path(args[0])); FileOutputFormat.setOutputPath(job, new Path(args[1])); System.exit(job.waitForCompletion(true) ? 0 : 1); } catch (IOException | InterruptedException | ClassNotFoundException ex) { System.out.println("Erorr Message" + ex.getMessage()); } }
From source file:AverageProj.AveragePrice.java
public int run(String[] args) throws Exception, ClassNotFoundException { Configuration conf = getConf(); Job job = new Job(conf, "Avg"); job.setJarByClass(AveragePrice.class); //final File f = new File(AveragePrice.class.getProtectionDomain().getCodeSource().getLocation().getPath()); Path in = new Path(args[0]); Path out = new Path(args[1]); FileInputFormat.setInputPaths(job, in); FileOutputFormat.setOutputPath(job, out); job.setMapperClass(AvMapper.class); job.setMapOutputKeyClass(YearPrice.class); job.setMapOutputValueClass(DoubleWritable.class); job.setGroupingComparatorClass(YearSymComparator.class); // job.setCombinerClass(AvReducer.class); job.setReducerClass(AvReducer.class); job.setInputFormatClass(TextInputFormat.class); job.setOutputFormatClass(TextOutputFormat.class); job.setOutputKeyClass(YearPrice.class); job.setOutputValueClass(DoubleWritable.class); job.setPartitionerClass(AvgPartitioner.class); job.setNumReduceTasks(7);/*from w ww . j a v a 2 s . co m*/ System.exit(job.waitForCompletion(true) ? 0 : 1); return 0; }
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 av a2 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;//from w w w . j a v a 2s . 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:clustering.link_back.step1.Driver.java
License:Apache License
public Job configJob(String[] args) throws Exception { if (args.length < 3) { System.err.printf("usage: %s mst_result_dir simhash_result_file output_dir\n", getClass().getSimpleName()); System.exit(1);/*from ww w . ja va 2 s .c o m*/ } Configuration conf = getConf(); conf = MapReduceUtils.initConf(conf); Job job = Job.getInstance(conf, "link back step 1 job"); job.setJarByClass(Driver.class); FileInputFormat.addInputPath(job, new Path(args[0])); FileInputFormat.addInputPath(job, new Path(args[1])); job.setInputFormatClass(KeyValueTextInputFormat.class); job.setMapperClass(SetKeyMapper.class); job.setMapOutputKeyClass(Step1KeyWritable.class); job.setMapOutputValueClass(Text.class); job.setPartitionerClass(JoinPartitioner.class); job.setGroupingComparatorClass(Step1GroupComparator.class); job.setReducerClass(JoinReducer.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(IntWritable.class); FileOutputFormat.setOutputPath(job, new Path(args[2])); return job; }
From source file:clustering.link_back.step2.Driver.java
License:Apache License
public Job configJob(String[] args) throws Exception { if (args.length < 3) { System.err.printf("usage: %s pre_step_result_dir step1_result_dir output_dir\n", getClass().getSimpleName()); System.exit(1);// w w w . java 2s. c o m } Configuration conf = getConf(); conf = MapReduceUtils.initConf(conf); Job job = Job.getInstance(conf, "link back step 2 job"); job.setJarByClass(Driver.class); FileInputFormat.addInputPath(job, new Path(args[0])); FileInputFormat.addInputPath(job, new Path(args[1])); job.setInputFormatClass(KeyValueTextInputFormat.class); job.setMapperClass(clustering.link_back.step2.SetKeyMapper.class); job.setMapOutputKeyClass(Step2KeyWritable.class); job.setMapOutputValueClass(Text.class); job.setPartitionerClass(JoinPartitioner.class); job.setGroupingComparatorClass(Step2GroupComparator.class); job.setReducerClass(clustering.link_back.step2.JoinReducer.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(IntWritable.class); FileOutputFormat.setOutputPath(job, new Path(args[2])); return job; }
From source file:com.asakusafw.runtime.mapreduce.simple.SimpleJobRunnerTest.java
License:Apache License
/** * Test for map-reduce job./* w ww.ja v a 2 s .c o m*/ * @throws Exception if failed */ @Test public void map_reduce() throws Exception { Job job = newJob(); job.setInputFormatClass(TextInputFormat.class); job.setOutputFormatClass(TextOutputFormat.class); job.setMapperClass(WordCountMapper.class); job.setMapOutputKeyClass(Text.class); job.setMapOutputValueClass(LongWritable.class); job.setSortComparatorClass(Text.Comparator.class); job.setGroupingComparatorClass(Text.Comparator.class); job.setReducerClass(WordCountReducer.class); job.setNumReduceTasks(1); job.setOutputKeyClass(Text.class); job.setOutputValueClass(LongWritable.class); File inputDir = folder.newFolder(); File inputFile = new File(inputDir, "input.txt"); write(inputFile, new String[] { "a b c d", "a a b c", "c", }); File outputDir = folder.newFolder(); outputDir.delete(); FileInputFormat.setInputPaths(job, new Path(inputFile.toURI())); FileOutputFormat.setOutputPath(job, new Path(outputDir.toURI())); assertThat(new SimpleJobRunner().run(job), is(true)); assertThat(toMap(read(outputDir)), is(map(new String[] { "a", "3", "b", "2", "c", "3", "d", "1", }))); }
From source file:com.asakusafw.runtime.stage.AbstractStageClient.java
License:Apache License
@SuppressWarnings("rawtypes") private void configureShuffle(Job job, VariableTable variables) { Class<? extends Reducer> reducer = getReducerClassOrNull(); if (reducer != null) { if (LOG.isDebugEnabled()) { LOG.debug(MessageFormat.format("Reducer: {0}", reducer.getName())); //$NON-NLS-1$ }// w ww .java2 s. com job.setReducerClass(reducer); } else { if (LOG.isDebugEnabled()) { LOG.debug("Reducer: N/A"); //$NON-NLS-1$ } job.setNumReduceTasks(0); return; } Class<? extends Writable> outputKeyClass = or(getShuffleKeyClassOrNull(), NullWritable.class); Class<? extends Writable> outputValueClass = or(getShuffleValueClassOrNull(), NullWritable.class); if (LOG.isDebugEnabled()) { LOG.debug(MessageFormat.format("Shuffle: key={0}, value={1}", //$NON-NLS-1$ outputKeyClass.getName(), outputValueClass.getName())); } job.setMapOutputKeyClass(outputKeyClass); job.setMapOutputValueClass(outputValueClass); Class<? extends Reducer> combiner = getCombinerClassOrNull(); if (combiner != null) { if (LOG.isDebugEnabled()) { LOG.debug(MessageFormat.format("Combiner: {0}", combiner.getName())); //$NON-NLS-1$ } job.setCombinerClass(combiner); } else { if (LOG.isDebugEnabled()) { LOG.debug("Combiner: N/A"); //$NON-NLS-1$ } } Class<? extends Partitioner> partitioner = getPartitionerClassOrNull(); if (partitioner != null) { if (LOG.isDebugEnabled()) { LOG.debug(MessageFormat.format("Partitioner: {0}", partitioner.getName())); //$NON-NLS-1$ } job.setPartitionerClass(partitioner); } else { if (LOG.isDebugEnabled()) { LOG.debug("Partitioner: DEFAULT"); //$NON-NLS-1$ } } Class<? extends RawComparator> groupingComparator = getGroupingComparatorClassOrNull(); if (groupingComparator != null) { if (LOG.isDebugEnabled()) { LOG.debug(MessageFormat.format("GroupingComparator: {0}", groupingComparator.getName())); //$NON-NLS-1$ } job.setGroupingComparatorClass(groupingComparator); } else { if (LOG.isDebugEnabled()) { LOG.debug("GroupingComparator: DEFAULT"); //$NON-NLS-1$ } } Class<? extends RawComparator> sortComparator = getSortComparatorClassOrNull(); if (sortComparator != null) { if (LOG.isDebugEnabled()) { LOG.debug(MessageFormat.format("SortComparator: {0}", sortComparator.getName())); //$NON-NLS-1$ } job.setSortComparatorClass(sortComparator); } else { if (LOG.isDebugEnabled()) { LOG.debug("SortComparator: DEFAULT"); //$NON-NLS-1$ } } }
From source file:com.asakusafw.thundergate.runtime.cache.mapreduce.CacheBuildClient.java
License:Apache License
private void updateMerge() throws IOException, InterruptedException { Job job = newJob(); List<StageInput> inputList = new ArrayList<>(); inputList.add(new StageInput(storage.getHeadContents("*").toString(), TemporaryInputFormat.class, MergeJoinBaseMapper.class)); inputList.add(new StageInput(storage.getPatchContents("*").toString(), TemporaryInputFormat.class, MergeJoinPatchMapper.class)); StageInputDriver.set(job, inputList); job.setInputFormatClass(StageInputFormat.class); job.setMapperClass(StageInputMapper.class); job.setMapOutputKeyClass(PatchApplyKey.class); job.setMapOutputValueClass(modelClass); // combiner may have no effect in normal cases job.setReducerClass(MergeJoinReducer.class); job.setOutputKeyClass(NullWritable.class); job.setOutputValueClass(modelClass); job.setPartitionerClass(PatchApplyKey.Partitioner.class); job.setSortComparatorClass(PatchApplyKey.SortComparator.class); job.setGroupingComparatorClass(PatchApplyKey.GroupComparator.class); TemporaryOutputFormat.setOutputPath(job, getNextDirectory()); job.setOutputFormatClass(TemporaryOutputFormat.class); job.getConfiguration().setClass("mapred.output.committer.class", LegacyBridgeOutputCommitter.class, org.apache.hadoop.mapred.OutputCommitter.class); LOG.info(MessageFormat.format("applying patch (merge join): {0} / {1} -> {2}", storage.getPatchContents("*"), storage.getHeadContents("*"), getNextContents())); try {// www .j av a2s . com boolean succeed = job.waitForCompletion(true); LOG.info(MessageFormat.format("applied patch (merge join): succeed={0}, {1} / {2} -> {3}", succeed, storage.getPatchContents("*"), storage.getHeadContents("*"), getNextContents())); if (succeed == false) { throw new IOException(MessageFormat.format("failed to apply patch (merge join): {0} / {1} -> {2}", storage.getPatchContents("*"), storage.getHeadContents("*"), getNextContents())); } } catch (ClassNotFoundException e) { throw new IOException(e); } putMeta(); }