runner/compbio/runner/_NativeSpecHelper.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \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.runner;\r
  19 \r
  20 import java.net.UnknownServiceException;\r
  21 \r
  22 import compbio.engine.cluster.dundee._Queue;\r
  23 \r
  24 public class _NativeSpecHelper {\r
  25 \r
  26         int maxCalculationTime;\r
  27         int requiredMemory;\r
  28         String queue;\r
  29 \r
  30         public _NativeSpecHelper(int requiredMemory) {\r
  31                 this(requiredMemory, 0);\r
  32         }\r
  33 \r
  34         public _NativeSpecHelper(int requiredMemory, int maxCalculationTime) {\r
  35                 this.requiredMemory = requiredMemory;\r
  36                 this.maxCalculationTime = maxCalculationTime;\r
  37         }\r
  38 \r
  39         public void setRequiredMemory(int memory) {\r
  40                 this.requiredMemory = memory;\r
  41         }\r
  42 \r
  43         int getRequiredMemory() {\r
  44                 return requiredMemory;\r
  45         }\r
  46 \r
  47         public void setQueue(String queue) {\r
  48                 this.queue = queue;\r
  49         }\r
  50 \r
  51         public String getQueue() {\r
  52                 return queue;\r
  53         }\r
  54 \r
  55         // -q 64bit.q -l qname=64bit.q -l h_vmem=8000M -l ram=8000M\r
  56         public String getNativeSpec() throws UnknownServiceException {\r
  57                 if (queue == null) {\r
  58                         queue = getApproprieteQueue().toString();\r
  59                 } else {\r
  60                         // check whether chosen queue suits for memory and runtime settings\r
  61                         _Queue knownQueue = _Queue.BIGINT.getQueue(queue);\r
  62                         if (knownQueue == null) {\r
  63                                 throw new UnknownServiceException("Queue " + queue\r
  64                                                 + " is not regestered in the system! ");\r
  65                         }\r
  66                         if (this.requiredMemory <= knownQueue.getMemoryLimit()) {\r
  67                                 throw new UnknownServiceException("Queue " + queue\r
  68                                                 + " has a memory limit of "\r
  69                                                 + knownQueue.getMemoryLimit()\r
  70                                                 + "M - which is smaller than requested!");\r
  71                         }\r
  72                         if (knownQueue.hasTimeLimit()\r
  73                                         && this.maxCalculationTime <= knownQueue.getTimeLimit()) {\r
  74                                 throw new UnknownServiceException("Queue " + queue\r
  75                                                 + " has a time limit of " + knownQueue.getTimeLimit()\r
  76                                                 + "hours - which is smaller than requested!");\r
  77                         }\r
  78                 }\r
  79                 return "-q " + queue.toString() + "-l qname=" + queue.toString()\r
  80                                 + ", h_vmem=" + requiredMemory + "M,ram=" + requiredMemory\r
  81                                 + "M";\r
  82         }\r
  83 \r
  84         public _Queue getApproprieteQueue() {\r
  85                 return _Queue.getQueue(requiredMemory, maxCalculationTime);\r
  86         }\r
  87 \r
  88 }\r