/** * start a vina hadoop job * * @param confLocalPath * @param receptorLocalPath * @param ligandPath * @param seed * @param topK * @param vinaJobID * @param node * @return */ public HashMap<String, String> startJob( String confLocalPath, String receptorLocalPath, ArrayList<String> ligandPath, String seed, int topK, String vinaJobID, int numPerNode, boolean verbose) { HashMap<String, String> hm = new HashMap<String, String>(); if (confLocalPath == null || receptorLocalPath == null || ligandPath == null || seed == null || vinaJobID == null || ligandPath.size() == 0 || topK < 0) { hm.put("flag", "false"); hm.put("hadoopID", "null"); hm.put("vinaJobID", vinaJobID); hm.put("log", "error arguments"); return hm; } GeneratePath gp = new GeneratePath(jobPath, srcDataPath); String confName = confLocalPath.substring(confLocalPath.lastIndexOf("/")); String confHDFSPath = jobPath + vinaJobID + confName; String receptorName = receptorLocalPath.substring(receptorLocalPath.lastIndexOf("/")); String receptorHDFSPATH = jobPath + vinaJobID + receptorName; HadoopFile hf; final String input = jobPath + vinaJobID + "/metadata"; final String output = jobPath + vinaJobID + "/order"; Path path = new Path(output); Configuration conf; FileSystem fs; Job job; try { gp.createMeta(ligandPath, vinaJobID, numPerNode); hf = new HadoopFile(); hf.mkdir(jobPath + "/" + vinaJobID + "/exception"); hf.mkdir(jobPath + "/" + vinaJobID + "/exceptionBackup"); hf.localToHadoop(confLocalPath, confHDFSPath); hf.localToHadoop(receptorLocalPath, receptorHDFSPATH); conf = (new HadoopConf()).getConf(); fs = FileSystem.get(conf); // set heart beat time 45min long milliSeconds = 45 * 60 * 1000; conf.setLong("mapred.task.timeout", milliSeconds); conf.set("vinaJobID", vinaJobID); conf.setInt("k", topK); conf.set("conf2HDFS", confHDFSPath); conf.set("receptorHDFS", receptorHDFSPATH); conf.set("seed", seed); if (fs.exists(path)) { fs.delete(path, true); } job = new Job(conf, vinaJobID); job.setNumReduceTasks(1); job.setJarByClass(VinaHadoop.class); job.setMapperClass(VinaMapper.class); job.setReducerClass(VinaReducer.class); job.setMapOutputKeyClass(DoubleWritable.class); job.setMapOutputValueClass(DataPair.class); job.setOutputKeyClass(DoubleWritable.class); job.setOutputValueClass(Text.class); FileInputFormat.addInputPath(job, new Path(input)); FileOutputFormat.setOutputPath(job, new Path(output)); } catch (IOException e) { // TODO Auto-generated catch block hm.put("flag", "false"); hm.put("hadoopID", "null"); hm.put("vinaJobID", vinaJobID); hm.put("log", e.getMessage()); return hm; } try { if (verbose) { // System.exit(job.waitForCompletion(true) ? 0 : 1); job.waitForCompletion(true); } else { job.submit(); } } catch (ClassNotFoundException | IOException | InterruptedException e) { // TODO Auto-generated catch block hm.put("flag", "false"); hm.put("hadoopID", "null"); hm.put("vinaJobID", vinaJobID); hm.put("log", e.getMessage()); return hm; } hm.put("flag", "true"); hm.put("hadoopID", job.getJobID().toString()); hm.put("vinaJobID", vinaJobID); hm.put("log", "null"); return hm; }