Java Code Examples for org.apache.hadoop.mapreduce.Job#setPartitionerClass()

The following examples show how to use org.apache.hadoop.mapreduce.Job#setPartitionerClass() . These examples are extracted from open source projects. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example 1
Source Project: big-c   File: CredentialsTestJob.java    License: Apache License 2.0 6 votes vote down vote up
public Job createJob() 
throws IOException {
  Configuration conf = getConf();
  conf.setInt(MRJobConfig.NUM_MAPS, 1);
  Job job = Job.getInstance(conf, "test");
  job.setNumReduceTasks(1);
  job.setJarByClass(CredentialsTestJob.class);
  job.setNumReduceTasks(1);
  job.setMapperClass(CredentialsTestJob.CredentialsTestMapper.class);
  job.setMapOutputKeyClass(IntWritable.class);
  job.setMapOutputValueClass(NullWritable.class);
  job.setReducerClass(CredentialsTestJob.CredentialsTestReducer.class);
  job.setInputFormatClass(SleepJob.SleepInputFormat.class);
  job.setPartitionerClass(SleepJob.SleepJobPartitioner.class);
  job.setOutputFormatClass(NullOutputFormat.class);
  job.setSpeculativeExecution(false);
  job.setJobName("test job");
  FileInputFormat.addInputPath(job, new Path("ignored"));
  return job;
}
 
Example 2
Source Project: rya   File: CopyTool.java    License: Apache License 2.0 6 votes vote down vote up
private void setupSplitsFile(final Job job, final TableOperations parentTableOperations, final String parentTableName, final String childTableName) throws Exception {
    final FileSystem fs = FileSystem.get(conf);
    fs.setPermission(getPath(baseOutputDir, childTableName), new FsPermission(FsAction.ALL, FsAction.ALL, FsAction.ALL));
    final Path splitsPath = getPath(baseOutputDir, childTableName, "splits.txt");
    final Collection<Text> splits = parentTableOperations.listSplits(parentTableName, 100);
    log.info("Creating splits file at: " + splitsPath);
    try (PrintStream out = new PrintStream(new BufferedOutputStream(fs.create(splitsPath)), false, StandardCharsets.UTF_8.name())) {
        for (final Text split : splits) {
            final String encoded = new String(Base64.encodeBase64(TextUtil.getBytes(split)), StandardCharsets.UTF_8);
            out.println(encoded);
        }
    }
    fs.setPermission(splitsPath, new FsPermission(FsAction.ALL, FsAction.ALL, FsAction.ALL));

    final String userDir = PathUtils.clean(System.getProperty("user.dir"));
    // The splits file has a symlink created in the user directory for some reason.
    // It might be better to copy the entire file for Windows but it doesn't seem to matter if
    // the user directory symlink is broken.
    java.nio.file.Files.deleteIfExists(new File(userDir, "splits.txt").toPath());
    //Files.copy(new File(splitsPath.toString()), new File(userDir, "splits.txt"));
    job.setPartitionerClass(KeyRangePartitioner.class);
    KeyRangePartitioner.setSplitFile(job, splitsPath.toString());
    job.setNumReduceTasks(splits.size() + 1);
}
 
Example 3
Source Project: MLHadoop   File: merge_results_driver.java    License: Apache License 2.0 6 votes vote down vote up
public static boolean runWithJob(Job job, String out_path) throws IOException, InterruptedException, ClassNotFoundException {
  job.setJarByClass(merge_results_driver.class);

  job.setJobName("Final Step: Merging results and creating separate LU decomposed components of input matrix");

  FileOutputFormat.setOutputPath(job, new Path(out_path));

  job.setMapperClass(lud.naiveGaussian.mergeResults.merge_results_mapper.class);
  job.setReducerClass(lud.naiveGaussian.mergeResults.merge_results_reducer.class);
  job.setMapOutputKeyClass(TextPair.class);
  job.setMapOutputValueClass(Text.class);
  job.setOutputKeyClass(TextPair.class);
  job.setOutputValueClass(Text.class);
  job.setPartitionerClass(TextPairPartitioner.class);
     job.setGroupingComparatorClass(NaturalKeyGroupingComparator.class);
     job.setSortComparatorClass(TextPairComparator.class);
     
     boolean success = job.waitForCompletion(true);
  return success;
}
 
Example 4
Source Project: kylin   File: ConvergeCuboidDataUtil.java    License: Apache License 2.0 6 votes vote down vote up
public static void setupReducer(Job job, CubeSegment cubeSegment, Path output) throws IOException {
    // Output
    //// prevent to create zero-sized default output
    LazyOutputFormat.setOutputFormatClass(job, SequenceFileOutputFormat.class);
    FileOutputFormat.setOutputPath(job, output);

    // Reducer
    job.setReducerClass(ConvergeCuboidDataReducer.class);
    job.setPartitionerClass(ConvergeCuboidDataPartitioner.class);
    job.setOutputKeyClass(Text.class);
    job.setOutputValueClass(Text.class);

    Pair<Integer, Integer> numReduceTasks = MapReduceUtil.getConvergeCuboidDataReduceTaskNums(cubeSegment);
    job.setNumReduceTasks(numReduceTasks.getFirst());

    int nBaseReduceTasks = numReduceTasks.getSecond();
    boolean enableSharding = cubeSegment.isEnableSharding();
    long baseCuboidId = cubeSegment.getCuboidScheduler().getBaseCuboidId();
    String partiParams = enableSharding + "," + baseCuboidId + "," + nBaseReduceTasks;
    job.getConfiguration().set(BatchConstants.CFG_CONVERGE_CUBOID_PARTITION_PARAM, partiParams);
}
 
Example 5
Source Project: kylin   File: HFileOutputFormat3.java    License: Apache License 2.0 5 votes vote down vote up
/**
 * Configure <code>job</code> with a TotalOrderPartitioner, partitioning against
 * <code>splitPoints</code>. Cleans up the partitions file after job exists.
 */
static void configurePartitioner(Job job, List<ImmutableBytesWritable> splitPoints) throws IOException {
    Configuration conf = job.getConfiguration();
    // create the partitions file
    FileSystem fs = FileSystem.get(conf);
    Path partitionsPath = new Path(conf.get("hbase.fs.tmp.dir"), "partitions_" + RandomUtil.randomUUID());
    fs.makeQualified(partitionsPath);
    writePartitions(conf, partitionsPath, splitPoints);
    fs.deleteOnExit(partitionsPath);

    // configure job to use it
    job.setPartitionerClass(TotalOrderPartitioner.class);
    TotalOrderPartitioner.setPartitionFile(conf, partitionsPath);
}
 
Example 6
Source Project: hadoop-arch-book   File: MRSessionize.java    License: Apache License 2.0 4 votes vote down vote up
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: MRSessionize <in> <out>");
        System.exit(2);
    }
    Job job = new Job(conf, "MapReduce Sessionization");
    job.setJarByClass(MRSessionize.class);
    job.setMapperClass(SessionizeMapper.class);
    job.setReducerClass(SessionizeReducer.class);

    // WARNING: do NOT set the Combiner class
    // from the same IP in one place before we can do sessionization
    // Also, our reducer doesn't return the same key,value types it takes
    // It can't be used on the result of a previous reducer

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

    // We need these for secondary sorting.
    // We need to shuffle the records (between Map and Reduce phases) by using IP address as key, since that is
    // the field we are using for determining uniqueness of users. However, when the records arrive to the reducers,
    // we would like them to be sorted in ascending order of their timestamps. This concept is known as secondary
    // sorting since we are "secondarily" sorting the records by another key (timestamp, in our case) in addition
    // to the shuffle key (also called the "partition" key).

    // So, to get some terminology straight.
    // Natural key (aka Shuffle key or Partition key) is the key we use to shuffle. IP address in our case
    // Secondary Sorting Key is the key we use to sort within each partition that gets sent to the user. Timestamp
    // in our case.
    // Together, the natural key and secondary sorting key form what we call the composite key. This key is called
    // IpTimestampKey in our example.

    // For secondary sorting, even though we are partitioning and shuffling by only the natural key, the map output
    // key and the reduce input key is the composite key. We, however, use a custom partitioner and custom grouping
    // comparator that only uses the natural key part of the composite key to partition and group respectively (both
    // happen during the shuffle phase).

    // However, we have a different sort comparator which also gets used in the shuffle phase but determines how
    // the records are sorted when they enter the reduce phase. This custom sort comparator in our case will make use
    // of the entire composite key.

    // We found http://vangjee.wordpress.com/2012/03/20/secondary-sorting-aka-sorting-values-in-hadoops-mapreduce-programming-paradigm/
    // to be very helpful, if you'd like to read more on the subject.
    job.setPartitionerClass(NaturalKeyPartitioner.class);
    job.setGroupingComparatorClass(NaturalKeyComparator.class);
    job.setSortComparatorClass(CompositeKeyComparator.class);

    FileInputFormat.addInputPath(job, new Path(otherArgs[0]));
    FileOutputFormat.setOutputPath(job, new Path(otherArgs[1]));
    System.exit(job.waitForCompletion(true) ? 0 : 1);
}
 
Example 7
Source Project: incubator-tez   File: TeraSort.java    License: Apache License 2.0 4 votes vote down vote up
public int run(String[] args) throws Exception {
  if (args.length != 2) {
    System.err.println("Invalid no. of arguments provided");
    System.err.println("Usage: terasort <input-dir> <output-dir>");
    return -1;
  }

  LOG.info("starting");
  Job job = Job.getInstance(getConf());
  Path inputDir = new Path(args[0]);
  Path outputDir = new Path(args[1]);
  boolean useSimplePartitioner = getUseSimplePartitioner(job);
  TeraInputFormat.setInputPaths(job, inputDir);
  FileOutputFormat.setOutputPath(job, outputDir);
  job.setJobName("TeraSort");
  job.setJarByClass(TeraSort.class);
  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);
  job.setInputFormatClass(TeraInputFormat.class);
  job.setOutputFormatClass(TeraOutputFormat.class);
  if (useSimplePartitioner) {
    job.setPartitionerClass(SimplePartitioner.class);
  } else {
    long start = System.currentTimeMillis();
    Path partitionFile = new Path(outputDir, 
                                  TeraInputFormat.PARTITION_FILENAME);
    URI partitionUri = new URI(partitionFile.toString() +
                               "#" + TeraInputFormat.PARTITION_FILENAME);
    try {
      TeraInputFormat.writePartitionFile(job, partitionFile);
    } catch (Throwable e) {
      LOG.error(e.getMessage());
      return -1;
    }
    job.addCacheFile(partitionUri);  
    long end = System.currentTimeMillis();
    System.out.println("Spent " + (end - start) + "ms computing partitions.");
    job.setPartitionerClass(TotalOrderPartitioner.class);
  }
  
  job.getConfiguration().setInt("dfs.replication", getOutputReplication(job));
  TeraOutputFormat.setFinalSync(job, true);
  int ret = job.waitForCompletion(true) ? 0 : 1;
  LOG.info("done");
  return ret;
}
 
Example 8
Source Project: tez   File: MRRSleepJob.java    License: Apache License 2.0 4 votes vote down vote up
@VisibleForTesting
public Job createJob(int numMapper, int numReducer, int iReduceStagesCount,
    int numIReducer, long mapSleepTime, int mapSleepCount,
    long reduceSleepTime, int reduceSleepCount,
    long iReduceSleepTime, int iReduceSleepCount)
        throws IOException {
  Configuration conf = getConf();
  conf.setLong(MAP_SLEEP_TIME, mapSleepTime);
  conf.setLong(REDUCE_SLEEP_TIME, reduceSleepTime);
  conf.setLong(IREDUCE_SLEEP_TIME, iReduceSleepTime);
  conf.setInt(MAP_SLEEP_COUNT, mapSleepCount);
  conf.setInt(REDUCE_SLEEP_COUNT, reduceSleepCount);
  conf.setInt(IREDUCE_SLEEP_COUNT, iReduceSleepCount);
  conf.setInt(MRJobConfig.NUM_MAPS, numMapper);
  conf.setInt(IREDUCE_STAGES_COUNT, iReduceStagesCount);
  conf.setInt(IREDUCE_TASKS_COUNT, numIReducer);

  // Configure intermediate reduces
  conf.setInt(
      org.apache.tez.mapreduce.hadoop.MRJobConfig.MRR_INTERMEDIATE_STAGES,
      iReduceStagesCount);
  LOG.info("Running MRR with " + iReduceStagesCount + " IR stages");

  for (int i = 1; i <= iReduceStagesCount; ++i) {
    // Set reducer class for intermediate reduce
    conf.setClass(
        MultiStageMRConfigUtil.getPropertyNameForIntermediateStage(i,
            "mapreduce.job.reduce.class"), ISleepReducer.class, Reducer.class);
    // Set reducer output key class
    conf.setClass(
        MultiStageMRConfigUtil.getPropertyNameForIntermediateStage(i,
            "mapreduce.map.output.key.class"), IntWritable.class, Object.class);
    // Set reducer output value class
    conf.setClass(
        MultiStageMRConfigUtil.getPropertyNameForIntermediateStage(i,
            "mapreduce.map.output.value.class"), IntWritable.class, Object.class);
    conf.setInt(
        MultiStageMRConfigUtil.getPropertyNameForIntermediateStage(i,
            "mapreduce.job.reduces"), numIReducer);
  }

  Job job = Job.getInstance(conf, "sleep");
  job.setNumReduceTasks(numReducer);
  job.setJarByClass(MRRSleepJob.class);
  job.setNumReduceTasks(numReducer);
  job.setMapperClass(SleepMapper.class);
  job.setMapOutputKeyClass(IntWritable.class);
  job.setMapOutputValueClass(IntWritable.class);
  job.setReducerClass(SleepReducer.class);
  job.setOutputFormatClass(NullOutputFormat.class);
  job.setInputFormatClass(SleepInputFormat.class);
  job.setPartitionerClass(MRRSleepJobPartitioner.class);
  job.setSpeculativeExecution(false);
  job.setJobName("Sleep job");

  FileInputFormat.addInputPath(job, new Path("ignored"));
  return job;
}
 
Example 9
Source Project: datawave   File: RowPartitioner.java    License: Apache License 2.0 4 votes vote down vote up
public static void configureJob(Job job) {
    job.setPartitionerClass(RowPartitioner.class);
}
 
Example 10
Source Project: hiped2   File: TotalSortMapReduce.java    License: Apache License 2.0 4 votes vote down vote up
/**
 * The MapReduce driver - setup and launch the job.
 *
 * @param args the command-line arguments
 * @return the process exit code
 * @throws Exception if something goes wrong
 */
public int run(final String[] args) throws Exception {

  int numReducers = 2;

  Cli cli = Cli.builder().setArgs(args).addOptions(CliOpts.values()).build();
  int result = cli.runCmd();

  if (result != 0) {
    return result;
  }

  Path input = new Path(cli.getArgValueAsString(CliOpts.INPUT));
  Path partitionFile = new Path(cli.getArgValueAsString(CliOpts.PARTITION));
  Path output = new Path(cli.getArgValueAsString(CliOpts.OUTPUT));


  InputSampler.Sampler<Text, Text> sampler =
      new InputSampler.RandomSampler<Text, Text>
          (0.1,
              10000,
              10);

  Configuration conf = super.getConf();

  Job job = new Job(conf);
  job.setJarByClass(TotalSortMapReduce.class);

  job.setNumReduceTasks(numReducers);

  job.setInputFormatClass(KeyValueTextInputFormat.class);
  job.setOutputFormatClass(TextOutputFormat.class);
  job.setPartitionerClass(TotalOrderPartitioner.class);

  job.setMapOutputKeyClass(Text.class);
  job.setMapOutputValueClass(Text.class);

  TotalOrderPartitioner.setPartitionFile(job.getConfiguration(), partitionFile);
  FileInputFormat.setInputPaths(job, input);
  FileOutputFormat.setOutputPath(job, output);

  InputSampler.writePartitionFile(job, sampler);

  URI partitionUri = new URI(partitionFile.toString() +
      "#" + "_sortPartitioning");
  DistributedCache.addCacheFile(partitionUri, conf);

  if (job.waitForCompletion(true)) {
    return 0;
  }
  return 1;
}
 
Example 11
Source Project: hiped2   File: CustomPartitionerJob.java    License: Apache License 2.0 4 votes vote down vote up
/**
 * The MapReduce driver - setup and launch the job.
 *
 * @param args the command-line arguments
 * @return the process exit code
 * @throws Exception if something goes wrong
 */
public int run(final String[] args) throws Exception {

  Cli cli = Cli.builder().setArgs(args).addOptions(IOOptions.values()).build();
  int result = cli.runCmd();

  if (result != 0) {
    return result;
  }

  Path input = new Path(cli.getArgValueAsString(IOOptions.INPUT));
  Path output = new Path(cli.getArgValueAsString(IOOptions.OUTPUT));

  Configuration conf = super.getConf();

  List<String> dates = Lists.newArrayList("2000-01-03",
      "2001-01-02", "2002-01-02", "2003-01-02", "2004-01-02",
      "2005-01-03", "2006-01-03", "2007-01-03", "2008-01-02",
      "2009-01-02");

  for (int partition = 0; partition < dates.size(); partition++) {
    DatePartitioner.addPartitionToConfig(conf,
        dates.get(partition), partition);
  }

  Job job = new Job(conf);
  job.setJarByClass(CustomPartitionerJob.class);
  job.setMapperClass(Map.class);
  job.setReducerClass(Reducer.class);

  job.setMapOutputKeyClass(Text.class);
  job.setMapOutputValueClass(Text.class);

  job.setPartitionerClass(DatePartitioner.class);

  FileInputFormat.setInputPaths(job, input);
  FileOutputFormat.setOutputPath(job, output);

  job.setNumReduceTasks(10);

  return job.waitForCompletion(true) ? 0 : 1;
}
 
Example 12
@Override
public int run(String[] args)
        throws Exception
{
    Job job = Job.getInstance(getConf());

    job.setJarByClass(Phase4RemoveDuplicatesUsingReduceSideJoins.class);
    job.setJobName(Phase4RemoveDuplicatesUsingReduceSideJoins.class.getName());

    // paths
    // text files of ids to be deleted
    String textFilePath = args[0];
    // corpus with *.warc.gz
    String commaSeparatedInputFiles = args[1];
    // output
    String outputPath = args[2];

    //second input the look up text file
    MultipleInputs.addInputPath(job, new Path(textFilePath), TextInputFormat.class,
            JoinTextMapper.class);
    //first input the data set (check comma separated availability)
    MultipleInputs.addInputPath(job, new Path(commaSeparatedInputFiles), WARCInputFormat.class,
            JoinWARCMapper.class);

    job.setPartitionerClass(SourceJoiningKeyPartitioner.class);
    job.setGroupingComparatorClass(SourceJoiningGroupingComparator.class);

    job.setMapOutputKeyClass(CompositeKey.class);
    job.setMapOutputValueClass(WARCWritable.class);

    job.setReducerClass(JoinReducer.class);

    job.setOutputFormatClass(WARCOutputFormat.class);
    job.setOutputKeyClass(NullWritable.class);
    job.setOutputValueClass(WARCWritable.class);
    FileOutputFormat.setOutputPath(job, new Path(outputPath));
    FileOutputFormat.setCompressOutput(job, true);
    FileOutputFormat.setOutputCompressorClass(job, GzipCodec.class);

    return job.waitForCompletion(true) ? 0 : 1;
}
 
Example 13
Source Project: MapReduce-Demo   File: TempSort.java    License: MIT License 4 votes vote down vote up
public static void main(String[] args) throws IOException, ClassNotFoundException, InterruptedException {
		// TODO Auto-generated method stub
		String hdfs = "hdfs://192.168.17.10:9000";
		Configuration conf = new Configuration();
		conf.set("fs.defaultFS", hdfs);
		conf.set("mapreduce.app-submission.cross-platform", "true");
		// 设置作业配置信息
		String jobName = "TempSort";
		Job job = Job.getInstance(conf, jobName);
		job.setJarByClass(TempSort.class);
		job.setJar("export\\TempSort.jar");
		// Map
		job.setMapperClass(TempSortMapper.class);
		job.setMapOutputKeyClass(Text.class);
		job.setMapOutputValueClass(IntWritable.class);
		// Reduce
		job.setReducerClass(TempSortReducer.class);
		// 全局
		job.setOutputKeyClass(Text.class);
		job.setOutputValueClass(IntWritable.class);
		// Sort
//		job.setSortComparatorClass(MySort.class);
		// Partition
		job.setPartitionerClass(YearPartitioner.class);
		job.setNumReduceTasks(3);
		//3.设置作业输入和输出路径
		String dataDir = "/expr/test/data";	//实验数据目录	
		String outputDir = "/expr/test/output";				//实验输出目录
		Path inPath = new Path(hdfs + dataDir);
		Path outPath = new Path(hdfs + outputDir);
		FileInputFormat.addInputPath(job, inPath);
		FileOutputFormat.setOutputPath(job, outPath);
		FileSystem fs = FileSystem.get(conf);
		if(fs.exists(outPath)) {
			fs.delete(outPath, true);
		}
		
		//4.运行作业
		System.out.println("Job: " + jobName + " is running...");
		if(job.waitForCompletion(true)) {
			System.out.println("success!");
			System.exit(0);
		} else {
			System.out.println("failed!");
			System.exit(1);
		}
	}
 
Example 14
Source Project: MapReduce-Demo   File: DatePartition.java    License: MIT License 4 votes vote down vote up
public static void main(String[] args) throws Exception {		
		//1.设置HDFS配置信息
		String namenode_ip = "192.168.17.10";
		String hdfs = "hdfs://" + namenode_ip + ":9000";			
		Configuration conf = new Configuration();
		conf.set("fs.defaultFS", hdfs);
		conf.set("mapreduce.app-submission.cross-platform", "true");

		//2.设置MapReduce作业配置信息
		String jobName = "DatePartition";					//定义作业名称
		Job job = Job.getInstance(conf, jobName);
		job.setJarByClass(DatePartition.class);				//指定运行时作业类
		job.setJar("export\\DatePartition.jar");			//指定本地jar包
//		Map
		job.setMapperClass(DatePartitionMapper.class);		//指定Mapper类
		job.setMapOutputKeyClass(Text.class);				//设置Mapper输出Key类型
		job.setMapOutputValueClass(IntWritable.class);		//设置Mapper输出Value类型
//		Reduce
		job.setReducerClass(DatePartitionReducer.class);	//指定Reducer类
//		全局
		job.setOutputKeyClass(Text.class);					//设置Reduce输出Key类型
		job.setOutputValueClass(IntWritable.class);			//设置Reduce输出Value类型
//		Partition
		job.setPartitionerClass(YearPartitioner.class);		//自定义分区方法
		job.setNumReduceTasks(10); 	//设置reduce任务的数量,该值传递给Partitioner.getPartition()方法的numPartitions参数
		
		//3.设置作业输入和输出路径
		String dataDir = "/expr/datecount/data";				//实验数据目录	
		String outputDir = "/expr/datecount/output_partition";	//实验输出目录
		Path inPath = new Path(hdfs + dataDir);
		Path outPath = new Path(hdfs + outputDir);
		FileInputFormat.addInputPath(job, inPath);
		FileOutputFormat.setOutputPath(job, outPath);
		FileSystem fs = FileSystem.get(conf);
		if(fs.exists(outPath)) {
			fs.delete(outPath, true);
		}
		
		//4.运行作业
		System.out.println("Job: " + jobName + " is running...");
		if(job.waitForCompletion(true)) {
			System.out.println("success!");
			System.exit(0);
		} else {
			System.out.println("failed!");
			System.exit(1);
		}
	}
 
Example 15
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;
    } else if(jobType == HalvadeResourceManager.DNA) {
        HalvadeResourceManager.setJobResources(halvadeOpts, halvadeConf, jobType, false, halvadeOpts.useBamInput);
        pipeline = DNA; 
    }
    halvadeOpts.splitChromosomes(halvadeConf, 0);
    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);     
    if(halvadeOpts.rnaPipeline)
        HalvadeConf.setPass2Suffix(halvadeConf, pass2suffix);
    
    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 && !halvadeOpts.mergeBam)
        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.countOnly) {
            halvadeJob.setReducerClass(be.ugent.intec.halvade.hadoop.mapreduce.CountReadsReducer.class);
            halvadeJob.setOutputValueClass(LongWritable.class);
        }
    }
    
    if(halvadeOpts.useBamInput) {
        halvadeJob.setMapperClass(be.ugent.intec.halvade.hadoop.mapreduce.AlignedBamMapper.class);
        halvadeJob.setInputFormatClass(BAMInputFormat.class);
    }
    
    return runTimedJob(halvadeJob, "Halvade Job");
}
 
Example 16
public int run(String[] args) throws Exception {
        //创建job
        Configuration config = getConf();
        //添加自定义配置
        config.addResource("mr.xml");
        Job job = Job.getInstance(config);
        //通过job设置一些参数
        //通过job设置一些参数
        job.setJarByClass(ParseLogJob.class);
        job.setJobName("parselog");
        job.setMapperClass(LogMapper.class);
        job.setReducerClass(LogReducer.class);
        job.setMapOutputKeyClass(TextLongWritable.class);
        job.setGroupingComparatorClass(TextLongGroupComparator.class);
        job.setPartitionerClass(TextLongPartition.class);
        job.setMapOutputValueClass(LogWritable.class);
        job.setOutputValueClass(Text.class);

        //设置CombineFileInputFormat
        job.setInputFormatClass(CombineTextInputFormat.class);

        //添加分布式缓存
        job.addCacheFile(new URI(config.get("ip.file.path")));

        //设置OutputFormat
        job.setOutputFormatClass(LogOutputFormat.class);


        //添加输入和输出数据
        FileInputFormat.addInputPath(job, new Path(args[0]));
        Path outputPath = new Path(args[1]);
        FileOutputFormat.setOutputPath(job, outputPath);


        //设置压缩类型
//        FileOutputFormat.setCompressOutput(job, true);
//        FileOutputFormat.setOutputCompressorClass(job, LzopCodec.class);

        FileSystem fs = FileSystem.get(config);
        if (fs.exists(outputPath)) {
            fs.delete(outputPath, true);
        }


        //运行程序
        if (!job.waitForCompletion(true)) {
            throw new RuntimeException(job.getJobName() + "failed!");
        }
        return 0;
    }
 
Example 17
Source Project: aegisthus   File: Aegisthus.java    License: Apache License 2.0 4 votes vote down vote up
@Override
public int run(String[] args) throws Exception {
    Job job = Job.getInstance(getConf());
    Configuration configuration = job.getConfiguration();

    job.setJarByClass(Aegisthus.class);
    CommandLine cl = getOptions(args);
    if (cl == null) {
        return 1;
    }

    // Check all of the paths and load the sstable version from the input filenames
    List<Path> paths = Lists.newArrayList();
    if (cl.hasOption(Feature.CMD_ARG_INPUT_FILE)) {
        for (String input : cl.getOptionValues(Feature.CMD_ARG_INPUT_FILE)) {
            paths.add(new Path(input));
        }
    }
    if (cl.hasOption(Feature.CMD_ARG_INPUT_DIR)) {
        paths.addAll(getDataFiles(configuration, cl.getOptionValue(Feature.CMD_ARG_INPUT_DIR)));
    }
    LOG.info("Processing paths: {}", paths);

    // At this point we have the version of sstable that we can use for this run
    Descriptor.Version version = Descriptor.Version.CURRENT;
    if (cl.hasOption(Feature.CMD_ARG_SSTABLE_OUTPUT_VERSION)) {
        version = new Descriptor.Version(cl.getOptionValue(Feature.CMD_ARG_SSTABLE_OUTPUT_VERSION));
    }
    configuration.set(Feature.CONF_SSTABLE_VERSION, version.toString());

    if (configuration.get(Feature.CONF_CQL_SCHEMA) != null) {
        setConfigurationFromCql(configuration);
    }

    if(cl.hasOption(Feature.CMD_ARG_COMBINE_SPLITS)) {
        job.setInputFormatClass(AegisthusCombinedInputFormat.class);
    } else {
        job.setInputFormatClass(AegisthusInputFormat.class);
    }
    job.setMapOutputKeyClass(AegisthusKey.class);
    job.setMapOutputValueClass(AtomWritable.class);
    job.setOutputKeyClass(AegisthusKey.class);
    job.setOutputValueClass(RowWritable.class);
    job.setMapperClass(AegisthusKeyMapper.class);
    job.setReducerClass(CassSSTableReducer.class);
    job.setGroupingComparatorClass(AegisthusKeyGroupingComparator.class);
    job.setPartitionerClass(AegisthusKeyPartitioner.class);
    job.setSortComparatorClass(AegisthusKeySortingComparator.class);

    TextInputFormat.setInputPaths(job, paths.toArray(new Path[paths.size()]));

    if (cl.hasOption(Feature.CMD_ARG_PRODUCE_SSTABLE)) {
        job.setOutputFormatClass(SSTableOutputFormat.class);
    } else {
        job.setOutputFormatClass(JsonOutputFormat.class);
    }
    CustomFileNameFileOutputFormat.setOutputPath(job, new Path(cl.getOptionValue(Feature.CMD_ARG_OUTPUT_DIR)));

    job.submit();
    if (configuration.getBoolean(Feature.CONF_SHUTDOWN_HOOK, true)) {
        Runtime.getRuntime().addShutdownHook(new JobKiller(job));
    }

    System.out.println(job.getJobID());
    System.out.println(job.getTrackingURL());
    boolean success = job.waitForCompletion(true);

    if (success) {
        Counter errorCounter = job.getCounters().findCounter("aegisthus", "error_skipped_input");
        long errorCount = errorCounter != null ? errorCounter.getValue() : 0L;
        int maxAllowed = configuration.getInt(Feature.CONF_MAX_CORRUPT_FILES_TO_SKIP, 0);
        if (errorCounter != null && errorCounter.getValue() > maxAllowed) {
            LOG.error("Found {} corrupt files which is greater than the max allowed {}", errorCount, maxAllowed);
            success = false;
        } else if (errorCount > 0) {
            LOG.warn("Found {} corrupt files but not failing the job because the max allowed is {}",
                    errorCount, maxAllowed);
        }
    }

    return success ? 0 : 1;
}
 
Example 18
public int run(String[] args) throws Exception {
        //创建job
        Configuration config = getConf();
        //添加自定义配置
        config.addResource("mr.xml");
        Job job = Job.getInstance(config);
        //通过job设置一些参数
        job.setJarByClass(ParseLogJob.class);
        job.setJobName("parselog");
        job.setMapperClass(LogMapper.class);
        job.setReducerClass(LogReducer.class);
        job.setMapOutputKeyClass(TextLongWritable.class);
        job.setGroupingComparatorClass(TextLongGroupComparator.class);
        job.setPartitionerClass(TextLongPartition.class);
        job.setMapOutputValueClass(LogWritable.class);
        job.setOutputValueClass(Text.class);

        //设置CombineFileInputFormat
        job.setInputFormatClass(CombineTextInputFormat.class);

        //添加分布式缓存
        job.addCacheFile(new URI(config.get("ip.file.path")));


        //添加输入和输出数据
        FileInputFormat.addInputPath(job, new Path(args[0]));
        Path outputPath = new Path(args[1]);
        FileOutputFormat.setOutputPath(job, outputPath);

        //设置压缩类型
//        FileOutputFormat.setCompressOutput(job, true);
//        FileOutputFormat.setOutputCompressorClass(job, LzopCodec.class);

        FileSystem fs = FileSystem.get(config);
        if (fs.exists(outputPath)) {
            fs.delete(outputPath, true);
        }


        //运行程序
        if (!job.waitForCompletion(true)) {
            throw new RuntimeException(job.getJobName() + "failed!");
        }
        return 0;
    }
 
Example 19
public int run(String[] args) throws Exception {
        //创建job
        Configuration config = getConf();
        //添加自定义配置
        config.addResource("mr.xml");
        Job job = Job.getInstance(config);
        //通过job设置一些参数
        job.setJarByClass(ParseLogJob.class);
        job.setJobName("parselog");
        job.setMapperClass(LogMapper.class);
        job.setReducerClass(LogReducer.class);
        job.setMapOutputKeyClass(TextLongWritable.class);
        job.setGroupingComparatorClass(TextLongGroupComparator.class);
        job.setPartitionerClass(TextLongPartition.class);
        job.setMapOutputValueClass(LogWritable.class);
        job.setOutputValueClass(Text.class);

        //添加分布式缓存
        job.addCacheFile(new URI(config.get("ip.file.path")));


        //添加输入和输出数据
        FileInputFormat.addInputPath(job, new Path(args[0]));
        Path outputPath = new Path(args[1]);
        FileOutputFormat.setOutputPath(job, outputPath);

        //设置压缩类型
//        FileOutputFormat.setCompressOutput(job, true);
//        FileOutputFormat.setOutputCompressorClass(job, LzopCodec.class);

        FileSystem fs = FileSystem.get(config);
        if (fs.exists(outputPath)) {
            fs.delete(outputPath, true);
        }


        //运行程序
        if (!job.waitForCompletion(true)) {
            throw new RuntimeException(job.getJobName() + "failed!");
        }
        return 0;
    }
 
Example 20
public int run(String[] args) throws Exception {
        //创建job
        Configuration config = getConf();
        //添加自定义配置
        config.addResource("mr.xml");
        Job job = Job.getInstance(config);
        //通过job设置一些参数
        job.setJarByClass(ParseLogJob.class);
        job.setJobName("parselog");
        job.setMapperClass(LogMapper.class);
        job.setReducerClass(LogReducer.class);
        job.setMapOutputKeyClass(TextLongWritable.class);
        job.setGroupingComparatorClass(TextLongGroupComparator.class);
        job.setPartitionerClass(TextLongPartition.class);
        job.setMapOutputValueClass(LogWritable.class);
        job.setOutputValueClass(Text.class);

        //设置CombineFileInputFormat
        job.setInputFormatClass(CombineTextInputFormat.class);

        //添加分布式缓存
        job.addCacheFile(new URI(config.get("ip.file.path")));

        //设置OutputFormat
        job.setOutputFormatClass(LogOutputFormat.class);

        //添加输入和输出数据
        FileInputFormat.addInputPath(job, new Path(args[0]));
        Path outputPath = new Path(args[1]);
        FileOutputFormat.setOutputPath(job, outputPath);

        //设置压缩类型
//        FileOutputFormat.setCompressOutput(job, true);
//        FileOutputFormat.setOutputCompressorClass(job, LzopCodec.class);

        FileSystem fs = FileSystem.get(config);
        if (fs.exists(outputPath)) {
            fs.delete(outputPath, true);
        }


        //运行程序
        if (!job.waitForCompletion(true)) {
            throw new RuntimeException(job.getJobName() + "failed!");
        }
        return 0;
    }