engine/compbio/engine/cluster/drmaa/ClusterUtil.java

   1 /* Copyright (c) 2009 Peter Troshin
   2  *
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
   4  *
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the
   6  *  Apache License version 2 as published by the Apache Software Foundation
   7  *
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
  10  *  License for more details.
  11  *
  12  *  A copy of the license is in apache_license.txt. It is also available here:
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
  14  *
  15  * Any republication or derived work distributed in source code form
  16  * must include this copyright and license notice.
  17  */
  18 package compbio.engine.cluster.drmaa;
  19
  20 import java.io.IOException;
  21 import java.text.NumberFormat;
  22
  23 import org.apache.log4j.Logger;
  24 import org.ggf.drmaa.DrmaaException;
  25 import org.ggf.drmaa.JobInfo;
  26 import org.ggf.drmaa.Session;
  27
  28 import compbio.engine.Configurator;
  29 import compbio.engine.client.Util;
  30 import compbio.metadata.JobExecutionException;
  31 import compbio.metadata.JobStatus;
  32
  33 public class ClusterUtil {
  34
  35         private static final Logger log = Logger.getLogger(ClusterUtil.class);
  36
  37         public static final NumberFormat CLUSTER_STAT_IN_SEC = NumberFormat
  38                         .getInstance();
  39
  40         static {
  41                 CLUSTER_STAT_IN_SEC.setMinimumFractionDigits(4);
  42         }
  43
  44         public static final boolean cancelJob(final String jobId,
  45                         ClusterSession csession) {
  46                 assert Util.isValidJobId(jobId);
  47                 boolean cancelled = true;
  48                 Session session = csession.getSession();
  49                 try {
  50                         log.info("Job " + jobId + " is successfully cancelled");
  51                         compbio.engine.client.Util.writeMarker(Configurator.getWorkDirectory(jobId),
  52                                         JobStatus.CANCELLED);
  53                         session.control(ClusterSession.getClusterJobId(jobId).getJobId(),
  54                                         Session.TERMINATE);
  55                 } catch (DrmaaException e) {
  56                         // Log silently
  57                         log.error("Job " + jobId + " cancellation failed!");
  58                         log.error("Cause: " + e.getLocalizedMessage(), e.getCause());
  59                         cancelled = false;
  60                 } catch (IOException e) {
  61                         log.error(
  62                                         "Could not read JOBID file to determine cluster jobid for taskid: "
  63                                                         + jobId + " Message: " + e.getLocalizedMessage(), e
  64                                                         .getCause());
  65                 } finally {
  66                         log
  67                                         .trace("Job "
  68                                                         + jobId
  69                                                         + " has been successfully removed from the cluster engine job list");
  70                         csession.removeJob(jobId);
  71                 }
  72                 return cancelled;
  73         }
  74
  75         public static final JobInfo waitForResult(ClusterSession csession,
  76                         String jobId) throws JobExecutionException {
  77                 JobInfo jinfo = null;
  78                 assert Util.isValidJobId(jobId);
  79                 try {
  80                         jinfo = csession.waitForJob(jobId);
  81                 } catch (DrmaaException e) {
  82                         log.error(e.getLocalizedMessage(), e.getCause());
  83                         throw new JobExecutionException(e);
  84                 } catch (IOException e) {
  85                         log.error("Could not read JOBID file for job " + jobId
  86                                         + " Message " + e.getMessage(), e.getCause());
  87                         throw new JobExecutionException(e);
  88                 } finally {
  89                         // at this point the job has finished
  90                         csession.removeJob(jobId);
  91                 }
  92                 return jinfo;
  93         }
  94
  95 }