Package pku.cbi.abcgrid.master

Examples of pku.cbi.abcgrid.master.Task

219
220
221
222
223
224
225
226
227
228
229
     * on Master's task queue. A broken connection may leads to RemoteException. 
     * */
    public static Task getTask(String service)
            throws RemoteException
    {
        Task task;
        while (true)
        {
            try
            {
                Status.set("idle");
View Full Code Here
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
        //    logger.debug("TaskRunnerThread started");
        while (true)
        {
            try
            {
                Task task = queue.take();
                //Future<Result> f = executor.submit(new TaskRunner(task));
                //Status.set("process task: "+service);
                String msg = String.format("[%d,%d], %s",
                        task.getJobId(),
                        task.getTaskId(),
                        Util.join(task.getCommand(), " "));
                if (Config.isVerbose())
                {
                    logger.info(msg);
                }
                Status.set("execute: " + msg);
View Full Code Here
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
    {
        AtomicLong task_id = new AtomicLong(1L);
        String user_dir = config.getUserDir(job.getSubmitter());
        List<Task> tasks = new ArrayList<Task>();
        //String[] taskcmd = removePathOfInputFile(job);
        Task t = new Task(
                job.getId(),
                task_id.getAndIncrement(),
                job.getServiceName(),
                job.getCommand(),
                job.getPriority(),
                0);
        Fragmentable frag = new PDB();
        for (TaskInput input : job.getInput())
        {
            File f = new File(user_dir, input.getName());
            int num_workers = WorkerManager.getInstance().getWorkerNum();
            num_workers = num_workers > 0 ? num_workers : 10;
            Object[] data = frag.fragment(f, num_workers);
            t.addInput(new TaskInput(input.getName(), data[0].toString().getBytes()));
        }
        tasks.add(t);
        return tasks;
    }
View Full Code Here
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
                num_workers = num_workers > 0 ? num_workers : 10;
                data = frag.fragment(new ByteArrayInputStream(input_data), num_workers);
                List<Task> tasks = new ArrayList<Task>(data.length);
                for (Object d : data)
                {
                    Task t = new Task(
                            job.getId(),
                            task_id.getAndIncrement(),
                            job.getServiceName(),
                            job.getCommand(),
                            job.getPriority(),
                            0);
                    t.addInput(new TaskInput(input_filename, d.toString().getBytes()));
                    tasks.add(t);
                }
                return tasks;
            }
            else//Task could have no any data. e.g. just use -h to print help message.
            {
                List<Task> tasks = new ArrayList<Task>(1);
                Task t = new Task(
                        job.getId(),
                        task_id.getAndIncrement(),
                        job.getServiceName(),
                        job.getCommand(),
                        job.getPriority(),
View Full Code Here
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
        public List<Task> call() throws Exception
        {
            AtomicLong task_id = new AtomicLong(1L);
            String user_dir = config.getUserDir(job.getSubmitter());
            List<Task> tasks = new ArrayList<Task>(1);
            Task t = new Task(
                    job.getId(),
                    task_id.getAndIncrement(),
                    job.getServiceName(),
                    job.getCommand(),
                    job.getPriority(),
                    0);
            for (TaskInput entry : job.getInput())
            {
                String fname = entry.getName();
                byte[] fdata = entry.getData();
                Fragmentable frag = FormatDetector.getFragmenter(new File(user_dir, fname));
                if (frag == null)
                    throw new Exception("Failed to  detect the format of input file:" + fname);
                Object[] data;
                int num_workers = WorkerManager.getInstance().getWorkerNum();
                num_workers = num_workers > 0 ? num_workers : 10;
                data = frag.fragment(new ByteArrayInputStream(fdata), num_workers);
                t.addInput(new TaskInput(fname, data[0].toString().getBytes()));
            }
            tasks.add(t);
            return tasks;
        }
View Full Code Here
46
47
48
49
50
51
52
53
54
55
56
    {
        try
        {
            while (!Thread.currentThread().isInterrupted())
            {
                Task t = MasterProxy.getTask(service);
                if (t != null)
                {
                    queue.put(t);
                }
            }
View Full Code Here
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
    {
        AtomicLong task_id = new AtomicLong(1L);
        String user_dir = config.getUserDir(job.getSubmitter());
        List<Task> tasks = new ArrayList<Task>();
        //String[] taskcmd = removePathOfInputFile(job);
        Task t = new Task(
                job.getId(),
                task_id.getAndIncrement(),
                job.getServiceName(),
                job.getCommand(),
                job.getPriority(),
                0);
        Fragmentable frag = new PDB();
        for (TaskInput input : job.getInput())
        {
            File f = new File(user_dir, input.getName());
            int num_workers = WorkerManager.getInstance().getWorkerNum();
            num_workers = num_workers > 0 ? num_workers : 10;
            Object[] data = frag.fragment(f, num_workers);
            t.addInput(new TaskInput(input.getName(), data[0].toString().getBytes()));
        }
        tasks.add(t);
        return tasks;
    }
View Full Code Here
TOP

Related Classes of pku.cbi.abcgrid.master.Task

  • pku.cbi.abcgrid.master.service.CE.CE
  • pku.cbi.abcgrid.master.service.DALI.DaliLite
  • pku.cbi.abcgrid.master.service.NCBI_BLAST.bl2seq$Fragmenter
  • pku.cbi.abcgrid.master.service.NCBI_BLAST.BlastallBase$Fragmenter
  • pku.cbi.abcgrid.worker.MasterProxy
  • pku.cbi.abcgrid.worker.TaskGetterThread
  • pku.cbi.abcgrid.worker.TaskRunnerThread
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.