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

The following examples show how to use org.apache.hadoop.mapreduce.Job#setSortComparatorClass() . 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: 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 2
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(lu_decomposition.naive_gausssian.MergeResults.merge_results_mapper.class);
  job.setReducerClass(lu_decomposition.naive_gausssian.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 3
Source Project: hiped2   File: Main.java    License: Apache License 2.0 6 votes vote down vote up
public static void runSortJob(Configuration conf, Path input, Path outputPath)
    throws Exception {

  Job job = new Job(conf);
  job.setJarByClass(Main.class);
  job.setMapperClass(SortMapReduce.Map.class);
  job.setReducerClass(SortMapReduce.Reduce.class);

  job.setInputFormatClass(KeyValueTextInputFormat.class);

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

  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);

  job.setPartitionerClass(PersonNamePartitioner.class);
  job.setSortComparatorClass(PersonComparator.class);
  job.setGroupingComparatorClass(PersonNameComparator.class);

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

  job.waitForCompletion(true);
}
 
Example 4
Source Project: rya   File: JoinSelectStatisticsTest.java    License: Apache License 2.0 5 votes vote down vote up
@Override
public int run(String[] args) throws Exception {

    Configuration conf = getConf();
    String outpath = conf.get(OUTPUTPATH);
    
    Job job = new Job(conf, this.getClass().getSimpleName() + "_" + System.currentTimeMillis());
    job.setJarByClass(this.getClass());
    conf.setBoolean(MRJobConfig.MAPREDUCE_JOB_USER_CLASSPATH_FIRST, true);
    
    MultipleInputs.addInputPath(job, new Path(PROSPECTSOUT.getAbsolutePath()), 
            SequenceFileInputFormat.class, JoinSelectAggregateMapper.class);
    MultipleInputs.addInputPath(job,new Path(SPOOUT.getAbsolutePath()) , 
            SequenceFileInputFormat.class, JoinSelectAggregateMapper.class);
    job.setMapOutputKeyClass(CompositeType.class);
    job.setMapOutputValueClass(TripleCard.class);

    tempDir = new File(File.createTempFile(outpath, "txt").getParentFile(), System.currentTimeMillis() + "");
    SequenceFileOutputFormat.setOutputPath(job, new Path(tempDir.getAbsolutePath()));
    job.setOutputFormatClass(SequenceFileOutputFormat.class);
    job.setOutputKeyClass(TripleEntry.class);
    job.setOutputValueClass(CardList.class);


    job.setSortComparatorClass(JoinSelectSortComparator.class);
    job.setGroupingComparatorClass(JoinSelectGroupComparator.class);
    job.setPartitionerClass(JoinSelectPartitioner.class);
    job.setReducerClass(JoinReducer.class);
    job.setNumReduceTasks(32);
    job.waitForCompletion(true);
    
    return job.isSuccessful() ? 0 : 1;          
}
 
Example 5
protected void configureMapper(Job job) {
  job.setInputFormatClass(OrcValueCombineFileInputFormat.class);
  job.setMapperClass(OrcValueMapper.class);
  job.setMapOutputKeyClass(OrcKey.class);
  job.setMapOutputValueClass(OrcValue.class);
  job.setGroupingComparatorClass(OrcKeyComparator.class);
  job.setSortComparatorClass(OrcKeyComparator.class);
}
 
Example 6
Source Project: hiped2   File: SortMapReduce.java    License: Apache License 2.0 5 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(CliCommonOpts.MrIoOpts.values()).build();
  int result = cli.runCmd();

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

  Path inputPath = new Path(cli.getArgValueAsString(CliCommonOpts.MrIoOpts.INPUT));
  Path outputPath = new Path(cli.getArgValueAsString(CliCommonOpts.MrIoOpts.OUTPUT));

  Configuration conf = super.getConf();
  Job job = new Job(conf);
  job.setJarByClass(SortMapReduce.class);

  job.setMapperClass(Map.class);
  job.setReducerClass(Reduce.class);

  job.setInputFormatClass(KeyValueTextInputFormat.class);

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

  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);

  job.setPartitionerClass(PersonNamePartitioner.class);
  job.setSortComparatorClass(PersonComparator.class);
  job.setGroupingComparatorClass(PersonNameComparator.class);

  FileInputFormat.setInputPaths(job, inputPath);
  FileOutputFormat.setOutputPath(job, outputPath);

  if (job.waitForCompletion(true)) {
    return 0;
  }
  return 1;
}
 
Example 7
Source Project: MapReduce-Demo   File: DateSortDesc.java    License: MIT License 4 votes vote down vote up
public static void main(String[] args) throws IOException, ClassNotFoundException, InterruptedException {
	// 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 = "DateSortDesc"; // 定义作业名称
	Job job = Job.getInstance(conf, jobName);
	job.setJarByClass(DateSortAsc.class); // 指定作业类
	job.setJar("export\\DateSortDesc.jar"); // 指定本地jar包

	job.setMapperClass(SortMapper.class);
	job.setMapOutputKeyClass(IntWritable.class);
	job.setMapOutputValueClass(Text.class);
	job.setReducerClass(SortReducer.class);
	job.setOutputKeyClass(Text.class);
	job.setOutputValueClass(IntWritable.class);
	// 指定排序所使用的比较器
	job.setSortComparatorClass(MyComparator.class);

	// 3.设置作业输入和输出路径
	String dataDir = "/workspace/dateSort/data"; // 实验数据目录
	String outputDir = "/workspace/dateSort/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 8
Source Project: MapReduce-Demo   File: DateSort2.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 = "DateSort2";					//定义作业名称
		Job job = Job.getInstance(conf, jobName);
		job.setJarByClass(DateSort2.class);				//指定作业类
		job.setJar("export\\DateSort2.jar");			//指定本地jar包
//		Map
		job.setMapperClass(DateSort2Mapper.class);		//指定Mapper类
		job.setMapOutputKeyClass(IntWritable.class);	//设置Mapper输出Key类型
		job.setMapOutputValueClass(Text.class);			//设置Mapper输出Value类型
//		Reduce
		job.setReducerClass(DateSort2Reducer.class);	//指定Reducer类
		job.setOutputKeyClass(Text.class);				//设置Reduce输出Key类型
		job.setOutputValueClass(IntWritable.class);		//设置Reduce输出Value类型
//		自定义Sort
		job.setSortComparatorClass(MySort.class);		//设置自定义排序类
		
		//3.设置作业输入和输出路径
		String dataDir = "/expr/datecount/output/part-r-00000";	//实验数据目录	
		String outputDir = "/expr/datecount/output_sort2";				//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 9
private void testComparator(String keySpec, int expect) 
    throws Exception {
  String root = System.getProperty("test.build.data", "/tmp");
  Path inDir = new Path(root, "test_cmp/in");
  Path outDir = new Path(root, "test_cmp/out");
  
  conf.set("mapreduce.partition.keycomparator.options", keySpec);
  conf.set("mapreduce.partition.keypartitioner.options", "-k1.1,1.1");
  conf.set(MRJobConfig.MAP_OUTPUT_KEY_FIELD_SEPERATOR, " ");

  Job job = MapReduceTestUtil.createJob(conf, inDir, outDir, 1, 1,
              line1 +"\n" + line2 + "\n"); 
  job.setMapperClass(InverseMapper.class);
  job.setReducerClass(Reducer.class);
  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(LongWritable.class);
  job.setSortComparatorClass(KeyFieldBasedComparator.class);
  job.setPartitionerClass(KeyFieldBasedPartitioner.class);

  job.waitForCompletion(true);
  assertTrue(job.isSuccessful());

  // validate output
  Path[] outputFiles = FileUtil.stat2Paths(getFileSystem().listStatus(outDir,
      new Utils.OutputFileUtils.OutputFilesFilter()));
  if (outputFiles.length > 0) {
    InputStream is = getFileSystem().open(outputFiles[0]);
    BufferedReader reader = new BufferedReader(new InputStreamReader(is));
    String line = reader.readLine();
    //make sure we get what we expect as the first line, and also
    //that we have two lines (both the lines must end up in the same
    //reducer since the partitioner takes the same key spec for all
    //lines
    if (expect == 1) {
      assertTrue(line.startsWith(line1));
    } else if (expect == 2) {
      assertTrue(line.startsWith(line2));
    }
    line = reader.readLine();
    if (expect == 1) {
      assertTrue(line.startsWith(line2));
    } else if (expect == 2) {
      assertTrue(line.startsWith(line1));
    }
    reader.close();
  }
}
 
Example 10
private void testComparator(String keySpec, int expect) 
    throws Exception {
  String root = System.getProperty("test.build.data", "/tmp");
  Path inDir = new Path(root, "test_cmp/in");
  Path outDir = new Path(root, "test_cmp/out");
  
  conf.set("mapreduce.partition.keycomparator.options", keySpec);
  conf.set("mapreduce.partition.keypartitioner.options", "-k1.1,1.1");
  conf.set(MRJobConfig.MAP_OUTPUT_KEY_FIELD_SEPERATOR, " ");

  Job job = MapReduceTestUtil.createJob(conf, inDir, outDir, 1, 1,
              line1 +"\n" + line2 + "\n"); 
  job.setMapperClass(InverseMapper.class);
  job.setReducerClass(Reducer.class);
  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(LongWritable.class);
  job.setSortComparatorClass(KeyFieldBasedComparator.class);
  job.setPartitionerClass(KeyFieldBasedPartitioner.class);

  job.waitForCompletion(true);
  assertTrue(job.isSuccessful());

  // validate output
  Path[] outputFiles = FileUtil.stat2Paths(getFileSystem().listStatus(outDir,
      new Utils.OutputFileUtils.OutputFilesFilter()));
  if (outputFiles.length > 0) {
    InputStream is = getFileSystem().open(outputFiles[0]);
    BufferedReader reader = new BufferedReader(new InputStreamReader(is));
    String line = reader.readLine();
    //make sure we get what we expect as the first line, and also
    //that we have two lines (both the lines must end up in the same
    //reducer since the partitioner takes the same key spec for all
    //lines
    if (expect == 1) {
      assertTrue(line.startsWith(line1));
    } else if (expect == 2) {
      assertTrue(line.startsWith(line2));
    }
    line = reader.readLine();
    if (expect == 1) {
      assertTrue(line.startsWith(line2));
    } else if (expect == 2) {
      assertTrue(line.startsWith(line1));
    }
    reader.close();
  }
}
 
Example 11
Source Project: hbase   File: IntegrationTestBulkLoad.java    License: Apache License 2.0 4 votes vote down vote up
/**
 * After adding data to the table start a mr job to
 * @throws IOException
 * @throws ClassNotFoundException
 * @throws InterruptedException
 */
private void runCheck() throws IOException, ClassNotFoundException, InterruptedException {
  LOG.info("Running check");
  Configuration conf = getConf();
  String jobName = getTablename() + "_check" + EnvironmentEdgeManager.currentTime();
  Path p = util.getDataTestDirOnTestFS(jobName);

  Job job = new Job(conf);
  job.setJarByClass(getClass());
  job.setJobName(jobName);

  job.setPartitionerClass(NaturalKeyPartitioner.class);
  job.setGroupingComparatorClass(NaturalKeyGroupingComparator.class);
  job.setSortComparatorClass(CompositeKeyComparator.class);

  Scan scan = new Scan();
  scan.addFamily(CHAIN_FAM);
  scan.addFamily(SORT_FAM);
  scan.readVersions(1);
  scan.setCacheBlocks(false);
  scan.setBatch(1000);

  int replicaCount = conf.getInt(NUM_REPLICA_COUNT_KEY, NUM_REPLICA_COUNT_DEFAULT);
  if (replicaCount != NUM_REPLICA_COUNT_DEFAULT) {
    scan.setConsistency(Consistency.TIMELINE);
  }

  TableMapReduceUtil.initTableMapperJob(
      getTablename().getName(),
      scan,
      LinkedListCheckingMapper.class,
      LinkKey.class,
      LinkChain.class,
      job
  );

  job.setReducerClass(LinkedListCheckingReducer.class);
  job.setOutputKeyClass(NullWritable.class);
  job.setOutputValueClass(NullWritable.class);

  FileOutputFormat.setOutputPath(job, p);

  assertEquals(true, job.waitForCompletion(true));

  // Delete the files.
  util.getTestFileSystem().delete(p, true);
}
 
Example 12
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 13
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 14
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 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
Source Project: hiped2   File: PersonSortMapReduce.java    License: Apache License 2.0 3 votes vote down vote up
public static void runSortJob(String input, String output)
    throws Exception {
  Configuration conf = new Configuration();

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

  job.setMapperClass(Map.class);
  job.setReducerClass(Reduce.class);

  job.setInputFormatClass(KeyValueTextInputFormat.class);

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

  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);

  job.setSortComparatorClass(PersonBinaryComparator.class);

  Path outputPath = new Path(output);

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

  outputPath.getFileSystem(conf).delete(outputPath, true);

  job.waitForCompletion(true);
}
 
Example 17
Source Project: hiped2   File: CloneReduce.java    License: Apache License 2.0 3 votes vote down vote up
public static void runSortJob(String input, String output)
    throws Exception {
  Configuration conf = new Configuration();

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

  job.setReducerClass(Reduce.class);

  job.setInputFormatClass(KeyValueTextInputFormat.class);

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

  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);

  job.setSortComparatorClass(PersonBinaryComparator.class);

  Path outputPath = new Path(output);

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

  outputPath.getFileSystem(conf).delete(outputPath, true);

  job.waitForCompletion(true);
}
 
Example 18
Source Project: hiped2   File: SampleMapReduce.java    License: Apache License 2.0 3 votes vote down vote up
public static void runSortJob(String input, String output)
    throws Exception {
  Configuration conf = new Configuration();

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

  job.setMapperClass(Map.class);
  job.setReducerClass(Reduce.class);

  job.setInputFormatClass(KeyValueTextInputFormat.class);

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

  job.setOutputKeyClass(Text.class);
  job.setOutputValueClass(Text.class);

  job.setPartitionerClass(PersonNamePartitioner.class);
  job.setSortComparatorClass(PersonComparator.class);
  job.setGroupingComparatorClass(PersonNameComparator.class);

  Path outputPath = new Path(output);

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

  outputPath.getFileSystem(conf).delete(outputPath, true);

  job.waitForCompletion(true);
}
 
Example 19
Source Project: BigDataArchitect   File: MyTopN.java    License: Apache License 2.0 2 votes vote down vote up
public static void main(String[] args) throws Exception {

        Configuration conf = new Configuration(true);

        conf.set("mapreduce.framework.name","local");
        conf.set("mapreduce.app-submission.cross-platform","true");


        String[] other = new GenericOptionsParser(conf, args).getRemainingArgs();

        Job  job = Job.getInstance(conf);
        job.setJarByClass(MyTopN.class);

        job.setJobName("TopN");

        job.setJar("C:\\Users\\Administrator\\IdeaProjects\\msbhadoop\\target\\hadoop-hdfs-1.0-0.1.jar");
        //客户端规划的时候讲join的右表cache到mapTask出现的节点上
        job.addCacheFile(new Path("/data/topn/dict/dict.txt").toUri());





        //初学者,关注的是client端的代码梳理:因为把这块写明白了,其实你也就真的知道这个作业的开发原理;

        //maptask
        //input

        TextInputFormat.addInputPath(job,new Path(other[0]));

        Path outPath = new Path(other[1]);

        if(outPath.getFileSystem(conf).exists(outPath))  outPath.getFileSystem(conf).delete(outPath,true);
        TextOutputFormat.setOutputPath(job,outPath);


        //key
        //map
        job.setMapperClass(TMapper.class);
        job.setMapOutputKeyClass(TKey.class);
        job.setMapOutputValueClass(IntWritable.class);

        //partitioner  按  年,月  分区  -》  分区 > 分组  按 年分区!!!!!!
            //分区器潜台词:满足  相同的key获得相同的分区号就可以~!
        job.setPartitionerClass(TPartitioner.class);
        //sortComparator  年,月,温度  且  温度倒序
        job.setSortComparatorClass(TSortComparator.class);
        //combine
//        job.setCombinerClass();




        //reducetask
        //groupingComparator
        job.setGroupingComparatorClass(TGroupingComparator.class);
        //reduce
        job.setReducerClass(TReducer.class);

        job.waitForCompletion(true);



    }
 
Example 20
Source Project: ignite   File: HadoopSortingTest.java    License: Apache License 2.0 2 votes vote down vote up
/**
     * @throws Exception If failed.
     */
    @Test
    public void testSortSimple() throws Exception {
        // Generate test data.
        Job job = Job.getInstance();

        job.setInputFormatClass(InFormat.class);

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

        job.setMapperClass(Mapper.class);
        job.setNumReduceTasks(0);

        setupFileSystems(job.getConfiguration());

        FileOutputFormat.setOutputPath(job, new Path(igfsScheme() + PATH_INPUT));

        X.printerrln("Data generation started.");

        grid(0).hadoop().submit(new HadoopJobId(UUID.randomUUID(), 1),
            createJobInfo(job.getConfiguration(), null)).get(180000);

        X.printerrln("Data generation complete.");

        // Run main map-reduce job.
        job = Job.getInstance();

        setupFileSystems(job.getConfiguration());

        job.getConfiguration().set(CommonConfigurationKeys.IO_SERIALIZATIONS_KEY, JavaSerialization.class.getName() +
            "," + WritableSerialization.class.getName());

        FileInputFormat.setInputPaths(job, new Path(igfsScheme() + PATH_INPUT));
        FileOutputFormat.setOutputPath(job, new Path(igfsScheme() + PATH_OUTPUT));

        job.setSortComparatorClass(JavaSerializationComparator.class);

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

        job.setNumReduceTasks(2);

        job.setMapOutputKeyClass(UUID.class);
        job.setMapOutputValueClass(NullWritable.class);

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

        X.printerrln("Job started.");

        grid(0).hadoop().submit(new HadoopJobId(UUID.randomUUID(), 2),
            createJobInfo(job.getConfiguration(), null)).get(180000);

        X.printerrln("Job complete.");

        // Check result.
        Path outDir = new Path(igfsScheme() + PATH_OUTPUT);

        AbstractFileSystem fs = AbstractFileSystem.get(new URI(igfsScheme()), job.getConfiguration());

        for (FileStatus file : fs.listStatus(outDir)) {
            X.printerrln("__ file: " + file);

            if (file.getLen() == 0)
                continue;

            FSDataInputStream in = fs.open(file.getPath());

            Scanner sc = new Scanner(in);

            UUID prev = null;

            while (sc.hasNextLine()) {
                UUID next = UUID.fromString(sc.nextLine());

//                X.printerrln("___ check: " + next);

                if (prev != null)
                    assertTrue(prev.compareTo(next) < 0);

                prev = next;
            }
        }
    }