/**
* 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;
}
