engine/compbio/engine/cluster/drmaa/_DrmaaExample.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.engine.cluster.drmaa;\r
  19 \r
  20 import java.util.Collections;\r
  21 import java.util.Iterator;\r
  22 import java.util.LinkedList;\r
  23 import java.util.List;\r
  24 \r
  25 import org.ggf.drmaa.DrmCommunicationException;\r
  26 import org.ggf.drmaa.DrmaaException;\r
  27 import org.ggf.drmaa.JobInfo;\r
  28 import org.ggf.drmaa.JobTemplate;\r
  29 import org.ggf.drmaa.Session;\r
  30 import org.ggf.drmaa.SessionFactory;\r
  31 \r
  32 class _DrmaaExample {\r
  33 \r
  34         private static int NBULKS = 3;\r
  35         private static int JOB_CHUNK = 8;\r
  36         private static Session session = null;\r
  37 \r
  38         public static void main(String[] args) throws Exception {\r
  39                 String jobPath = args[0];\r
  40 \r
  41                 SessionFactory factory = SessionFactory.getFactory();\r
  42 \r
  43                 session = factory.getSession();\r
  44                 session.init(null);\r
  45 \r
  46                 JobTemplate jt = createJobTemplate(jobPath, 5, true);\r
  47 \r
  48                 List allJobIds = new LinkedList();\r
  49                 List jobIds = null;\r
  50                 boolean retry = true;\r
  51 \r
  52                 for (int count = 0; count < NBULKS; count++) {\r
  53                         do {\r
  54                                 try {\r
  55                                         jobIds = session.runBulkJobs(jt, 1, JOB_CHUNK, 1);\r
  56                                         retry = false;\r
  57                                 } catch (DrmCommunicationException e) {\r
  58                                         System.err.println("runBulkJobs() failed - retry: "\r
  59                                                         + e.getMessage());\r
  60 \r
  61                                         Thread.sleep(1000);\r
  62                                 }\r
  63                         } while (retry);\r
  64 \r
  65                         allJobIds.addAll(jobIds);\r
  66 \r
  67                         System.out.println("submitted bulk job with jobids:");\r
  68 \r
  69                         Iterator i = jobIds.iterator();\r
  70 \r
  71                         while (i.hasNext()) {\r
  72                                 System.out.println("\t \"" + i.next() + "\"");\r
  73                         }\r
  74                 }\r
  75 \r
  76                 session.deleteJobTemplate(jt);\r
  77 \r
  78                 /* submit some sequential jobs */\r
  79                 jt = createJobTemplate(jobPath, 5, false);\r
  80 \r
  81                 String jobId = null;\r
  82                 retry = true;\r
  83 \r
  84                 for (int count = 0; count < JOB_CHUNK; count++) {\r
  85                         while (retry) {\r
  86                                 try {\r
  87                                         jobId = session.runJob(jt);\r
  88                                         retry = false;\r
  89                                 } catch (DrmCommunicationException e) {\r
  90                                         System.err.println("runBulkJobs() failed - retry: "\r
  91                                                         + e.getMessage());\r
  92 \r
  93                                         Thread.sleep(1000);\r
  94                                 }\r
  95                         }\r
  96 \r
  97                         System.out.println("\t \"" + jobId + "\"");\r
  98                         allJobIds.add(jobId);\r
  99                 }\r
 100 \r
 101                 session.deleteJobTemplate(jt);\r
 102 \r
 103                 /* synchronize with all jobs */\r
 104                 session.synchronize(allJobIds, Session.TIMEOUT_WAIT_FOREVER, false);\r
 105                 System.out.println("synchronized with all jobs");\r
 106 \r
 107                 /* wait all those jobs */\r
 108                 Iterator i = allJobIds.iterator();\r
 109 \r
 110                 while (i.hasNext()) {\r
 111                         JobInfo status = null;\r
 112                         jobId = (String) i.next();\r
 113 \r
 114                         status = session.wait(jobId, Session.TIMEOUT_WAIT_FOREVER);\r
 115 \r
 116                         /* report how job finished */\r
 117                         if (status.wasAborted()) {\r
 118                                 System.out.println("job \"" + jobId + "\" never ran");\r
 119                         } else if (status.hasExited()) {\r
 120                                 System.out.println("job \"" + jobId\r
 121                                                 + "\" finished regularly with exit status "\r
 122                                                 + status.getExitStatus());\r
 123                         } else if (status.hasSignaled()) {\r
 124                                 System.out.println("job \"" + jobId\r
 125                                                 + "\" finished due to signal "\r
 126                                                 + status.getTerminatingSignal());\r
 127                         } else {\r
 128                                 System.out.println("job \"" + jobId\r
 129                                                 + "\" finished with unclear conditions");\r
 130                         }\r
 131                 }\r
 132         }\r
 133 \r
 134         private static JobTemplate createJobTemplate(String jobPath, int seconds,\r
 135                         boolean isBulkJob) throws DrmaaException {\r
 136                 JobTemplate jt = session.createJobTemplate();\r
 137 \r
 138                 jt.setWorkingDirectory("$drmaa_hd_ph$");\r
 139                 jt.setRemoteCommand(jobPath);\r
 140                 jt.setArgs(Collections.singletonList(Integer.toString(seconds)));\r
 141                 jt.setJoinFiles(true);\r
 142 \r
 143                 if (!isBulkJob) {\r
 144                         jt.setOutputPath(":$drmaa_hd_ph$/DRMAA_JOB");\r
 145                 } else {\r
 146                         jt.setOutputPath(":$drmaa_hd_ph$/DRMAA_JOB$drmaa_incr_ph$");\r
 147                 }\r
 148 \r
 149                 return jt;\r
 150         }\r
 151 \r
 152 }\r