org.apache.hadoop.mapreduce.Job#addCacheArchive ( )源码实例Demo

下面列出了org.apache.hadoop.mapreduce.Job#addCacheArchive ( ) 实例代码，或者点击链接到github查看源代码，也可以在右侧发表评论。

源代码1 项目： incubator-pinot 文件： HadoopSegmentGenerationJobRunner.java

protected void packPluginsToDistributedCache(Job job) {
  String pluginsRootDir = PluginManager.get().getPluginsRootDir();
  if (new File(pluginsRootDir).exists()) {
    File pluginsTarGzFile = new File(PINOT_PLUGINS_TAR_GZ);
    try {
      TarGzCompressionUtils.createTarGzOfDirectory(pluginsRootDir, pluginsTarGzFile.getPath());
    } catch (IOException e) {
      LOGGER.error("Failed to tar plugins directory", e);
      throw new RuntimeException(e);
    }
    job.addCacheArchive(pluginsTarGzFile.toURI());

    String pluginsIncludes = System.getProperty(PLUGINS_INCLUDE_PROPERTY_NAME);
    if (pluginsIncludes != null) {
      job.getConfiguration().set(PLUGINS_INCLUDE_PROPERTY_NAME, pluginsIncludes);
    }
  } else {
    LOGGER.warn("Cannot find local Pinot plugins directory at [{}]", pluginsRootDir);
  }
}

源代码2 项目： incubator-pinot 文件： HadoopSegmentGenerationJobRunner.java

protected void addDepsJarToDistributedCache(Job job, String depsJarDir)
    throws IOException {
  if (depsJarDir != null) {
    URI depsJarDirURI = URI.create(depsJarDir);
    if (depsJarDirURI.getScheme() == null) {
      depsJarDirURI = new File(depsJarDir).toURI();
    }
    PinotFS pinotFS = PinotFSFactory.create(depsJarDirURI.getScheme());
    String[] files = pinotFS.listFiles(depsJarDirURI, true);
    for (String file : files) {
      URI fileURI = URI.create(file);
      if (!pinotFS.isDirectory(fileURI)) {
        if (file.endsWith(".jar")) {
          LOGGER.info("Adding deps jar: {} to distributed cache", file);
          job.addCacheArchive(fileURI);
        }
      }
    }
  }
}

源代码3 项目： hadoop 文件： TestMRWithDistributedCache.java

private void testWithConf(Configuration conf) throws IOException,
    InterruptedException, ClassNotFoundException, URISyntaxException {
  // Create a temporary file of length 1.
  Path first = createTempFile("distributed.first", "x");
  // Create two jars with a single file inside them.
  Path second =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.second.jar"), 2);
  Path third =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.third.jar"), 3);
  Path fourth =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.fourth.jar"), 4);


  Job job = Job.getInstance(conf);
  job.setMapperClass(DistributedCacheCheckerMapper.class);
  job.setReducerClass(DistributedCacheCheckerReducer.class);
  job.setOutputFormatClass(NullOutputFormat.class);
  FileInputFormat.setInputPaths(job, first);
  // Creates the Job Configuration
  job.addCacheFile(
    new URI(first.toUri().toString() + "#distributed.first.symlink"));
  job.addFileToClassPath(second);
  job.addArchiveToClassPath(third);
  job.addCacheArchive(fourth.toUri());
  job.setMaxMapAttempts(1); // speed up failures

  job.submit();
  assertTrue(job.waitForCompletion(false));
}

源代码4 项目： big-c 文件： TestMRWithDistributedCache.java

private void testWithConf(Configuration conf) throws IOException,
    InterruptedException, ClassNotFoundException, URISyntaxException {
  // Create a temporary file of length 1.
  Path first = createTempFile("distributed.first", "x");
  // Create two jars with a single file inside them.
  Path second =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.second.jar"), 2);
  Path third =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.third.jar"), 3);
  Path fourth =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.fourth.jar"), 4);


  Job job = Job.getInstance(conf);
  job.setMapperClass(DistributedCacheCheckerMapper.class);
  job.setReducerClass(DistributedCacheCheckerReducer.class);
  job.setOutputFormatClass(NullOutputFormat.class);
  FileInputFormat.setInputPaths(job, first);
  // Creates the Job Configuration
  job.addCacheFile(
    new URI(first.toUri().toString() + "#distributed.first.symlink"));
  job.addFileToClassPath(second);
  job.addArchiveToClassPath(third);
  job.addCacheArchive(fourth.toUri());
  job.setMaxMapAttempts(1); // speed up failures

  job.submit();
  assertTrue(job.waitForCompletion(false));
}

源代码5 项目： incubator-pinot 文件： PinotHadoopJobPreparationHelper.java

public static void addDepsJarToDistributedCacheHelper(FileSystem fileSystem, Job job, Path depsJarDir)
    throws IOException {
  FileStatus[] fileStatuses = fileSystem.listStatus(depsJarDir);
  for (FileStatus fileStatus : fileStatuses) {
    if (fileStatus.isDirectory()) {
      addDepsJarToDistributedCacheHelper(fileSystem, job, fileStatus.getPath());
    } else {
      Path depJarPath = fileStatus.getPath();
      if (depJarPath.getName().endsWith(".jar")) {
        _logger.info("Adding deps jar: {} to distributed cache", depJarPath);
        job.addCacheArchive(depJarPath.toUri());
      }
    }
  }
}

源代码6 项目： hadoop 文件： TestMRJobs.java

public void _testDistributedCache(String jobJarPath) throws Exception {
  if (!(new File(MiniMRYarnCluster.APPJAR)).exists()) {
    LOG.info("MRAppJar " + MiniMRYarnCluster.APPJAR
         + " not found. Not running test.");
    return;
  }

  // Create a temporary file of length 1.
  Path first = createTempFile("distributed.first", "x");
  // Create two jars with a single file inside them.
  Path second =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.second.jar"), 2);
  Path third =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.third.jar"), 3);
  Path fourth =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.fourth.jar"), 4);

  Job job = Job.getInstance(mrCluster.getConfig());
  
  // Set the job jar to a new "dummy" jar so we can check that its extracted 
  // properly
  job.setJar(jobJarPath);
  // Because the job jar is a "dummy" jar, we need to include the jar with
  // DistributedCacheChecker or it won't be able to find it
  Path distributedCacheCheckerJar = new Path(
          JarFinder.getJar(DistributedCacheChecker.class));
  job.addFileToClassPath(distributedCacheCheckerJar.makeQualified(
          localFs.getUri(), distributedCacheCheckerJar.getParent()));
  
  job.setMapperClass(DistributedCacheChecker.class);
  job.setOutputFormatClass(NullOutputFormat.class);

  FileInputFormat.setInputPaths(job, first);
  // Creates the Job Configuration
  job.addCacheFile(
      new URI(first.toUri().toString() + "#distributed.first.symlink"));
  job.addFileToClassPath(second);
  // The AppMaster jar itself
  job.addFileToClassPath(
          APP_JAR.makeQualified(localFs.getUri(), APP_JAR.getParent())); 
  job.addArchiveToClassPath(third);
  job.addCacheArchive(fourth.toUri());
  job.setMaxMapAttempts(1); // speed up failures

  job.submit();
  String trackingUrl = job.getTrackingURL();
  String jobId = job.getJobID().toString();
  Assert.assertTrue(job.waitForCompletion(false));
  Assert.assertTrue("Tracking URL was " + trackingUrl +
                    " but didn't Match Job ID " + jobId ,
        trackingUrl.endsWith(jobId.substring(jobId.lastIndexOf("_")) + "/"));
}

源代码7 项目： big-c 文件： TestMRJobs.java

public void _testDistributedCache(String jobJarPath) throws Exception {
  if (!(new File(MiniMRYarnCluster.APPJAR)).exists()) {
    LOG.info("MRAppJar " + MiniMRYarnCluster.APPJAR
         + " not found. Not running test.");
    return;
  }

  // Create a temporary file of length 1.
  Path first = createTempFile("distributed.first", "x");
  // Create two jars with a single file inside them.
  Path second =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.second.jar"), 2);
  Path third =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.third.jar"), 3);
  Path fourth =
      makeJar(new Path(TEST_ROOT_DIR, "distributed.fourth.jar"), 4);

  Job job = Job.getInstance(mrCluster.getConfig());
  
  // Set the job jar to a new "dummy" jar so we can check that its extracted 
  // properly
  job.setJar(jobJarPath);
  // Because the job jar is a "dummy" jar, we need to include the jar with
  // DistributedCacheChecker or it won't be able to find it
  Path distributedCacheCheckerJar = new Path(
          JarFinder.getJar(DistributedCacheChecker.class));
  job.addFileToClassPath(distributedCacheCheckerJar.makeQualified(
          localFs.getUri(), distributedCacheCheckerJar.getParent()));
  
  job.setMapperClass(DistributedCacheChecker.class);
  job.setOutputFormatClass(NullOutputFormat.class);

  FileInputFormat.setInputPaths(job, first);
  // Creates the Job Configuration
  job.addCacheFile(
      new URI(first.toUri().toString() + "#distributed.first.symlink"));
  job.addFileToClassPath(second);
  // The AppMaster jar itself
  job.addFileToClassPath(
          APP_JAR.makeQualified(localFs.getUri(), APP_JAR.getParent())); 
  job.addArchiveToClassPath(third);
  job.addCacheArchive(fourth.toUri());
  job.setMaxMapAttempts(1); // speed up failures

  job.submit();
  String trackingUrl = job.getTrackingURL();
  String jobId = job.getJobID().toString();
  Assert.assertTrue(job.waitForCompletion(false));
  Assert.assertTrue("Tracking URL was " + trackingUrl +
                    " but didn't Match Job ID " + jobId ,
        trackingUrl.endsWith(jobId.substring(jobId.lastIndexOf("_")) + "/"));
}

源代码8 项目： halvade 文件： MapReduceRunner.java

protected int runPass1RNAJob(Configuration pass1Conf, String tmpOutDir) throws IOException, InterruptedException, ClassNotFoundException, URISyntaxException {
    HalvadeConf.setIsPass2(pass1Conf, false);
    HalvadeResourceManager.setJobResources(halvadeOpts, pass1Conf, HalvadeResourceManager.RNA_SHMEM_PASS1, halvadeOpts.nodes == 1, halvadeOpts.useBamInput);
    int pass2Reduces = HalvadeResourceManager.getPass2Reduces(halvadeOpts);
    halvadeOpts.splitChromosomes(pass1Conf, pass2Reduces);
    HalvadeConf.setPass2Suffix(pass1Conf, pass2suffix);
    
    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);
    // set pass 2 suffix so only this job finds it!
    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;
}

源代码9 项目： halvade 文件： MapReduceRunner.java

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");
}