List of usage examples for org.apache.hadoop.mapreduce Job setJarByClass
public void setJarByClass(Class<?> cls)
From source file:Distinct.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: Distinct <in> <out>"); System.exit(2);// ww w .j a va2 s . co m } Job job = Job.getInstance(conf, "distinct1"); job.setJarByClass(Distinct.class); job.setMapperClass(TokenizerMapper1.class); job.setReducerClass(Reducer1.class); FileInputFormat.addInputPath(job, new Path(otherArgs[0])); FileOutputFormat.setOutputPath(job, new Path(tempDir)); job.setOutputKeyClass(Text.class); job.setOutputValueClass(IntWritable.class); job.waitForCompletion(true); Configuration conf2 = new Configuration(); Job job2 = Job.getInstance(conf2, "distinct2"); job2.setJarByClass(Distinct.class); job2.setMapperClass(TokenizerMapper2.class); job2.setReducerClass(Reducer2.class); FileInputFormat.addInputPath(job2, new Path(tempDir)); FileOutputFormat.setOutputPath(job2, new Path(otherArgs[1])); job2.setOutputKeyClass(Text.class); job2.setOutputValueClass(IntWritable.class); System.exit(job2.waitForCompletion(true) ? 0 : 1); }
From source file:BigBWA.java
License:Open Source License
@Override public int run(String[] args) throws Exception { Configuration conf = this.getConf(); for (String argumento : args) { LOG.info("Arg: " + argumento); }//from www . j a va2 s .c om String inputPath = ""; String outputPath = ""; boolean useReducer = false; BwaOptions options = new BwaOptions(args); //We set the timeout and stablish the bwa library to call BWA methods conf.set("mapreduce.task.timeout", "0"); conf.set("mapreduce.map.env", "LD_LIBRARY_PATH=./bwa.zip/"); //==================Algorithm election================== //One of the algorithms is going to be in use, because tge default is always specified. if (options.isMemAlgorithm()) { //Case of the mem algorithm conf.set("mem", "true"); conf.set("aln", "false"); conf.set("bwasw", "false"); } else if (options.isAlnAlgorithm()) { // Case of aln algorithm conf.set("mem", "false"); conf.set("aln", "true"); conf.set("bwasw", "false"); } else if (options.isBwaswAlgorithm()) { // Case of bwasw algorithm conf.set("mem", "false"); conf.set("aln", "false"); conf.set("bwasw", "true"); } //==================Index election================== if (options.getIndexPath() != "") { conf.set("indexRoute", options.getIndexPath()); } else { System.err.println("No index has been found. Aborting."); System.exit(1); } //==================Type of reads election================== //There is always going to be a type of reads, because default is paired if (options.isPairedReads()) { conf.set("paired", "true"); conf.set("single", "false"); } else if (options.isSingleReads()) { conf.set("paired", "false"); conf.set("single", "true"); } //==================Use of reducer================== if (options.isUseReducer()) { useReducer = true; conf.set("useReducer", "true"); } else { conf.set("useReducer", "false"); } //==================Number of threads per map================== if (options.getNumThreads() != "0") { conf.set("bwathreads", options.getNumThreads()); } //==================RG Header=================== if (options.getReadgroupHeader() != "") { conf.set("rgheader", options.getReadgroupHeader()); } //==================Input and output paths================== inputPath = options.getInputPath(); outputPath = options.getOutputPath(); conf.set("outputGenomics", outputPath); //==================Partition number================== if (options.getPartitionNumber() != 0) { try { FileSystem fs = FileSystem.get(conf); Path inputFilePath = new Path(inputPath); ContentSummary cSummary = fs.getContentSummary(inputFilePath); long length = cSummary.getLength(); fs.close(); conf.set("mapreduce.input.fileinputformat.split.maxsize", String.valueOf((length) / options.getPartitionNumber())); conf.set("mapreduce.input.fileinputformat.split.minsize", String.valueOf((length) / options.getPartitionNumber())); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); LOG.error(e.toString()); System.exit(1); } } //Job job = new Job(conf,"BigBWA_"+outputPath); Job job = Job.getInstance(conf, "BigBWA_" + outputPath); job.setJarByClass(BigBWA.class); job.setMapperClass(BigBWAMap.class); //job.setCombinerClass(BigBWACombiner.class); if (useReducer) { job.setReducerClass(BigBWAReducer.class); job.setMapOutputKeyClass(IntWritable.class); job.setMapOutputValueClass(Text.class); job.setNumReduceTasks(1); } else { job.setNumReduceTasks(0); } job.setOutputKeyClass(NullWritable.class); job.setOutputValueClass(Text.class); FileInputFormat.addInputPath(job, new Path(inputPath)); FileOutputFormat.setOutputPath(job, new Path(outputPath)); return (job.waitForCompletion(true) ? 0 : 1); }
From source file:BigramRelativeFrequencyTuple.java
License:Apache License
/** * Runs this tool.//from ww w .j a v a 2s .c o m */ public int run(String[] args) throws Exception { if (args.length != 3) { printUsage(); return -1; } String inputPath = args[0]; String outputPath = args[1]; int reduceTasks = Integer.parseInt(args[2]); LOG.info("Tool name: " + BigramRelativeFrequencyTuple.class.getSimpleName()); LOG.info(" - input path: " + inputPath); LOG.info(" - output path: " + outputPath); LOG.info(" - num reducers: " + reduceTasks); Job job = Job.getInstance(getConf()); job.setJobName(BigramRelativeFrequencyTuple.class.getSimpleName()); job.setJarByClass(BigramRelativeFrequencyTuple.class); job.setNumReduceTasks(reduceTasks); FileInputFormat.setInputPaths(job, new Path(inputPath)); FileOutputFormat.setOutputPath(job, new Path(outputPath)); job.setMapOutputKeyClass(BinSedesTuple.class); job.setMapOutputValueClass(FloatWritable.class); job.setOutputKeyClass(BinSedesTuple.class); job.setOutputValueClass(FloatWritable.class); job.setOutputFormatClass(SequenceFileOutputFormat.class); job.setMapperClass(MyMapper.class); job.setCombinerClass(MyCombiner.class); job.setReducerClass(MyReducer.class); job.setPartitionerClass(MyPartitioner.class); // Delete the output directory if it exists already. Path outputDir = new Path(outputPath); FileSystem.get(getConf()).delete(outputDir, true); long startTime = System.currentTimeMillis(); job.waitForCompletion(true); System.out.println("Job Finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds"); return 0; }
From source file:WordCountA.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: wordcount <in> [<in>...] <out>"); System.exit(2);//from w ww . j a va 2 s.co m } Job job = Job.getInstance(conf, "word count"); job.setJarByClass(WordCountA.class); job.setMapperClass(TokenizerMapper.class); // Disable the combiner // job.setCombinerClass(IntSumReducer.class); // Setup the Partitioner job.setPartitionerClass(Letterpartitioner.class); job.setReducerClass(IntSumReducer.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(IntWritable.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:a.b.c.MultiFileWordCount.java
License:Apache License
public int run(String[] args) throws Exception { if (args.length < 2) { printUsage();//from w w w. j a v a 2 s . c o m return 2; } Job job = new Job(getConf()); job.setJobName("MultiFileWordCount"); job.setJarByClass(MultiFileWordCount.class); //set the InputFormat of the job to our InputFormat job.setInputFormatClass(MyInputFormat.class); // the keys are words (strings) job.setOutputKeyClass(Text.class); // the values are counts (ints) job.setOutputValueClass(IntWritable.class); //use the defined mapper job.setMapperClass(MapClass.class); //use the WordCount Reducer job.setCombinerClass(IntSumReducer.class); job.setReducerClass(IntSumReducer.class); FileInputFormat.addInputPaths(job, args[0]); FileOutputFormat.setOutputPath(job, new Path(args[1])); return job.waitForCompletion(true) ? 0 : 1; }
From source file:accesslog2.Accesslog2.java
public static void main(String[] args) throws Exception { Configuration conf = new Configuration(); Path inputPath = new Path(args[0]); Path outputPath = new Path(args[1]); Job job = Job.getInstance(conf, "Accesslog2"); job.setJarByClass(Accesslog2.class); job.setMapperClass(TokenizerMapper.class); job.setCombinerClass(IntSumReducer.class); job.setReducerClass(IntSumReducer.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(IntWritable.class); FileInputFormat.addInputPath(job, inputPath); FileOutputFormat.setOutputPath(job, outputPath); job.setInputFormatClass(TextInputFormat.class); job.setOutputFormatClass(TextOutputFormat.class); System.exit(job.waitForCompletion(true) ? 0 : 1); }
From source file:accesslog3.Accesslog3.java
public static void main(String[] args) throws Exception { Configuration conf = new Configuration(); Path inputPath = new Path(args[0]); Path outputPath = new Path(args[1]); Job job = Job.getInstance(conf, "Accesslog3"); job.setJarByClass(Accesslog3.class); job.setMapperClass(TokenizerMapper.class); job.setCombinerClass(IntSumReducer.class); job.setReducerClass(IntSumReducer.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(IntWritable.class); FileInputFormat.addInputPath(job, inputPath); FileOutputFormat.setOutputPath(job, outputPath); job.setInputFormatClass(TextInputFormat.class); job.setOutputFormatClass(TextOutputFormat.class); System.exit(job.waitForCompletion(true) ? 0 : 1); }
From source file:accesslog4.Accesslog4.java
public static void main(String[] args) throws Exception { Configuration conf = new Configuration(); Path inputPath = new Path(args[0]); Path outputPath = new Path(args[1]); Job job = Job.getInstance(conf, "Accesslog4"); job.setJarByClass(Accesslog4.class); job.setMapperClass(TokenizerMapper.class); job.setCombinerClass(IntSumReducer.class); job.setReducerClass(IntSumReducer.class); job.setOutputKeyClass(Text.class); job.setOutputValueClass(IntWritable.class); FileInputFormat.addInputPath(job, inputPath); FileOutputFormat.setOutputPath(job, outputPath); job.setInputFormatClass(TextInputFormat.class); job.setOutputFormatClass(TextOutputFormat.class); System.exit(job.waitForCompletion(true) ? 0 : 1); }
From source file:accismus.benchmark.Generator.java
License:Apache License
@Override public int run(String[] args) throws Exception { if (args.length != 3) { System.err.println(/*from www .j a va 2 s . com*/ "Usage : " + this.getClass().getSimpleName() + " <props file> <num task> <num documents>"); return 1; } Job job = new Job(getConf(), this.getClass().getSimpleName() + "_" + System.currentTimeMillis()); job.setJarByClass(this.getClass()); job.setInputFormatClass(DocumentInputFormat.class); DocumentInputFormat.setNumTask(job, Integer.parseInt(args[1]), Integer.parseInt(args[2])); job.setMapOutputKeyClass(Loader.class); job.setMapOutputValueClass(NullWritable.class); job.setMapperClass(GMapper.class); job.setNumReduceTasks(0); job.setOutputFormatClass(AccismusOutputFormat.class); Properties accisumusProps = new Properties(); accisumusProps.load(new FileReader(args[0])); AccismusOutputFormat.configure(job, accisumusProps); job.waitForCompletion(true); return 0; }
From source file:accismus.benchmark.Verifier.java
License:Apache License
@Override public int run(String[] args) throws Exception { if (args.length != 2) { System.err.println("Usage : " + this.getClass().getSimpleName() + " <props file> <output dir>"); return 1; }// ww w . ja v a 2s .c o m Job job = new Job(getConf(), this.getClass().getSimpleName() + "_" + System.currentTimeMillis()); job.setJarByClass(this.getClass()); AccismusProperties accisumusProps = new AccismusProperties(new File(args[0])); AccismusInputFormat.configure(job, accisumusProps); AccismusInputFormat.fetchFamilies(job, KEY, DUP); job.setInputFormatClass(AccismusInputFormat.class); job.setMapOutputKeyClass(Text.class); job.setMapOutputValueClass(Text.class); job.setMapperClass(VMapper.class); job.setReducerClass(VReducer.class); job.setOutputFormatClass(TextOutputFormat.class); TextOutputFormat.setOutputPath(job, new Path(args[1])); job.waitForCompletion(true); return 0; }