| 1 | # ---------------------------------------------------------------------- |
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| 2 | # |
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| 3 | # ====================================================================== |
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| 4 | # AUTHOR: Derrick Kearney, Purdue University |
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| 5 | # Copyright (c) 2005 Purdue Research Foundation, West Lafayette, IN |
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| 6 | # ====================================================================== |
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| 7 | |
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| 8 | import sys,os |
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| 9 | import re |
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| 10 | import time |
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| 11 | import shutil |
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| 12 | import datetime |
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| 13 | |
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| 14 | # import Rappture Related libs |
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| 15 | from tools import * |
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| 16 | |
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| 17 | ####################################################################### |
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| 18 | |
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| 19 | # http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/52235 |
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| 20 | class CallbaseError(AttributeError): |
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| 21 | pass |
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| 22 | |
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| 23 | def callbase(obj, base, methodname='__init__', args=(), raiseIfMissing=None): |
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| 24 | try: method = getattr(base, methodname) |
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| 25 | except AttributeError: |
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| 26 | if raiseIfMissing: |
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| 27 | raise CallbaseError, methodname |
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| 28 | return None |
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| 29 | if args is None: args = () |
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| 30 | return method(obj, *args) |
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| 31 | |
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| 32 | class RpQueueError(Exception): |
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| 33 | pass |
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| 34 | |
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| 35 | class queue: |
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| 36 | |
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| 37 | def __init__(self): |
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| 38 | |
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| 39 | # initialize the general queue variable with safe, default values |
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| 40 | self._queue_vars = {} |
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| 41 | self.__initQueueVars__() |
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| 42 | |
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| 43 | def __initQueueVars__(self): |
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| 44 | self._queue_vars['walltime'] = 1 |
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| 45 | self._queue_vars['resultsDir'] = "" |
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| 46 | self._queue_vars['executable'] = "" |
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| 47 | self._queue_vars['execArgs'] = "" |
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| 48 | self._queue_vars['nodes'] = 1 |
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| 49 | self._queue_vars['ppn'] = 1 |
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| 50 | self._queue_vars['queue'] = "" |
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| 51 | self._queue_vars['outFile'] = "" |
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| 52 | self._queue_vars['errFile'] = "" |
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| 53 | self._queue_vars['logFile'] = "" |
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| 54 | self._queue_vars['jobName'] = "" |
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| 55 | |
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| 56 | def walltime(self,walltime=''): |
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| 57 | walltime = str(walltime) |
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| 58 | if (walltime == '') or (walltime == 'None'): |
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| 59 | return self._queue_vars['walltime'] |
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| 60 | elif re.match(r'^\d{2}:\d{2}:\d{2}',walltime): |
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| 61 | self._queue_vars['walltime'] = walltime |
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| 62 | else: |
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| 63 | error = "Incorrect walltime format: should be 00:00:00" |
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| 64 | raise RpQueueError,error |
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| 65 | |
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| 66 | # walltime = str(walltime) |
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| 67 | # if re.match(r'^\d{2}:\d{2}:\d{2}',walltime): |
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| 68 | # else: |
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| 69 | # try: |
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| 70 | # walltime = int(walltime) |
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| 71 | # except: |
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| 72 | # error = "walltime must match format" |
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| 73 | # if (walltime <= 0): |
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| 74 | # return self._queue_vars['walltime'] |
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| 75 | # else: |
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| 76 | # self._queue_vars['walltime'] = walltime |
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| 77 | |
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| 78 | def resultsDir(self,resultsDir=''): |
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| 79 | resultsDir = str(resultsDir) |
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| 80 | if (resultsDir == 'None') or (resultsDir == ''): |
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| 81 | return self._queue_vars['resultsDir'] |
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| 82 | else: |
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| 83 | self._queue_vars['resultsDir'] = resultsDir |
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| 84 | |
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| 85 | def executable(self,executable=''): |
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| 86 | executable = str(executable) |
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| 87 | if (executable == 'None') or (executable == ''): |
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| 88 | return self._queue_vars['executable'] |
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| 89 | else: |
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| 90 | self._queue_vars['executable'] = executable |
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| 91 | |
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| 92 | def execArgs(self,execArgs=''): |
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| 93 | execArgs = str(execArgs) |
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| 94 | if (execArgs == 'None') or (execArgs == ''): |
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| 95 | return self._queue_vars['execArgs'] |
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| 96 | else: |
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| 97 | self._queue_vars['execArgs'] = execArgs |
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| 98 | |
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| 99 | def nodes(self,nodes=''): |
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| 100 | if nodes == '': |
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| 101 | return self._queue_vars['nodes'] |
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| 102 | nodes = int(nodes) |
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| 103 | if nodes > 0: |
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| 104 | self._queue_vars['nodes'] = nodes |
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| 105 | else: |
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| 106 | error = 'nodes must be a positive integer' |
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| 107 | raise RpQueueError, error |
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| 108 | |
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| 109 | def ppn(self,ppn=''): |
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| 110 | if ppn == '': |
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| 111 | return self._queue_vars['ppn'] |
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| 112 | ppn = int(ppn) |
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| 113 | if ppn > 0: |
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| 114 | self._queue_vars['ppn'] = ppn |
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| 115 | else: |
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| 116 | error = 'ppn must be a positive integer' |
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| 117 | raise RpQueueError, error |
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| 118 | |
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| 119 | def queue(self,queue=''): |
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| 120 | queue = str(queue) |
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| 121 | if (queue == 'None') or (queue == ''): |
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| 122 | return self._queue_vars['queue'] |
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| 123 | else : |
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| 124 | self._queue_vars['queue'] = queue |
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| 125 | |
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| 126 | def outFile(self,outFile=''): |
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| 127 | outFile = str(outFile) |
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| 128 | if (outFile == 'None') or (outFile == ''): |
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| 129 | return self._queue_vars['outFile'] |
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| 130 | else: |
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| 131 | self._queue_vars['outFile'] = outFile |
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| 132 | |
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| 133 | def errFile(self,errFile=''): |
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| 134 | errFile = str(errFile) |
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| 135 | if (errFile == 'None') or (errFile == ''): |
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| 136 | return self._queue_vars['errFile'] |
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| 137 | else: |
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| 138 | self._queue_vars['errFile'] = errFile |
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| 139 | |
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| 140 | def logFile(self,logFile=''): |
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| 141 | logFile = str(logFile) |
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| 142 | if (logFile == 'None') or (logFile == ''): |
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| 143 | return self._queue_vars['logFile'] |
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| 144 | else: |
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| 145 | self._queue_vars['logFile'] = logFile |
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| 146 | |
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| 147 | def jobName(self,jobName=''): |
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| 148 | jobName = str(jobName) |
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| 149 | if jobName == 'None' or (jobName == ''): |
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| 150 | return self._queue_vars['jobName'] |
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| 151 | else: |
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| 152 | self._queue_vars['jobName'] = jobName |
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| 153 | |
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| 154 | def transferFiles(self,transferFiles=[]): |
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| 155 | transferFiles = list(transferFiles) |
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| 156 | if (len(transferFiles) == 0) or (jobName == []): |
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| 157 | return self._queue_vars['transferFiles'] |
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| 158 | else: |
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| 159 | self._queue_vars['transferFiles'] = transferFiles |
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| 160 | |
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| 161 | def __convertWalltime__(self): |
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| 162 | pass |
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| 163 | |
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| 164 | def submit(self): |
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| 165 | pass |
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| 166 | |
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| 167 | def __checkFiles__(self,chkFileName): |
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| 168 | retVal = False |
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| 169 | if not os.path.isfile(chkFileName): |
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| 170 | retVal = True |
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| 171 | return retVal |
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| 172 | |
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| 173 | def status(self): |
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| 174 | min = 0 |
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| 175 | tCount = 0 |
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| 176 | sleepTime = 10 |
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| 177 | |
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| 178 | while self.__checkFiles__(self.errFile()): |
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| 179 | if tCount == 60 : |
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| 180 | min += 1 |
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| 181 | tCount = 0 |
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| 182 | |
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| 183 | self._currStatus = self.getCurrentStatus() |
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| 184 | if (self._currStatus != self._prevStatus): |
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| 185 | sys.stdout.write("%s: %s\n" % ( self._currStatus, time.ctime() ) ) |
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| 186 | sys.stdout.flush() |
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| 187 | self._prevStatus = self._currStatus |
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| 188 | |
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| 189 | time.sleep(sleepTime) |
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| 190 | tCount += sleepTime |
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| 191 | |
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| 192 | class pbs(queue): |
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| 193 | """the pbs class organizes the information needed to submit jobs to |
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| 194 | nanohub's pbs queues through Rappture""" |
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| 195 | |
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| 196 | def __init__( self, |
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| 197 | jobName, |
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| 198 | resultsDir, |
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| 199 | nodes, |
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| 200 | executable, |
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| 201 | execArgs='', |
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| 202 | walltime='00:01:00' ): |
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| 203 | |
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| 204 | # call the base class's init |
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| 205 | for base in self.__class__.__bases__: |
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| 206 | callbase(self, base) |
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| 207 | |
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| 208 | self._pbs_msgs = {} |
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| 209 | self.__fillStatusDict__() |
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| 210 | |
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| 211 | # initialize pbs script vars |
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| 212 | self._pbs_vars = {} |
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| 213 | self.__initPbsScriptVars__() |
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| 214 | |
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| 215 | # initialize jobId for this object |
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| 216 | self._jobId = "" |
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| 217 | |
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| 218 | # set vars based on user input |
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| 219 | self.resultsDir(resultsDir) |
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| 220 | self.jobName(jobName) |
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| 221 | self.nodes(nodes) |
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| 222 | self.walltime(walltime) |
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| 223 | self.executable(executable) |
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| 224 | self.execArgs(execArgs) |
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| 225 | nanoHUBQ = os.getenv("NANOHUB_PBS_QUEUE") |
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| 226 | if nanoHUBQ is None : |
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| 227 | self.queue("@vma118.punch.purdue.edu") |
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| 228 | else: |
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| 229 | self.queue(nanoHUBQ) |
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| 230 | |
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| 231 | def __initPbsScriptVars__(self): |
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| 232 | self._pbs_vars['cmd'] = "" |
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| 233 | |
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| 234 | def __fillStatusDict__(self): |
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| 235 | # Possible PBS Job States |
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| 236 | # From qstat manpage on hamlet.rcac.purdue.edu |
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| 237 | # E - Job is exiting after having run. |
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| 238 | # H - Job is held. |
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| 239 | # Q - job is queued, eligible to run or routed. |
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| 240 | # R - job is running. |
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| 241 | # T - job is being moved to new location. |
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| 242 | # W - job is waiting for its execution time |
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| 243 | # (-a option) to be reached. |
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| 244 | # S - job is suspended. |
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| 245 | |
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| 246 | self._pbs_msgs['E'] = 'Job is exiting after having run' |
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| 247 | self._pbs_msgs['H'] = 'Job is held' |
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| 248 | self._pbs_msgs['Q'] = 'Simulation Queued' |
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| 249 | self._pbs_msgs['R'] = 'Running Simulation' |
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| 250 | self._pbs_msgs['T'] = 'Job is being moved to new location. Please Wait...' |
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| 251 | self._pbs_msgs['W'] = 'Job is waiting for its execution time. Please Wait...' |
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| 252 | self._pbs_msgs['S'] = 'Job is suspended' |
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| 253 | self._pbs_msgs['DEFAULT'] = 'Returning Results...' |
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| 254 | |
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| 255 | def __makePbsScript__(self): |
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| 256 | # create the directory where output should be placed |
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| 257 | self._resultDirPath = os.path.join(os.getcwd(),self.resultsDir()) |
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| 258 | |
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| 259 | # if os.path.exists(self._resultDirPath): |
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| 260 | # shutil.rmtree(self._resultDirPath) |
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| 261 | # os.mkdir(self._resultDirPath) |
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| 262 | |
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| 263 | # set the out and err files |
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| 264 | if self.outFile() == '': |
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| 265 | self.outFile(os.path.join(self.resultsDir(),self.jobName()+".out")) |
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| 266 | |
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| 267 | if self.errFile() == '': |
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| 268 | self.errFile(os.path.join(self.resultsDir(),self.jobName()+".err")) |
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| 269 | |
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| 270 | # remove existing "FLAG" files if they exist |
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| 271 | if os.path.isfile(self.outFile()): |
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| 272 | os.remove(self.outFile()) |
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| 273 | if os.path.isfile(self.errFile()): |
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| 274 | os.remove(self.errFile()) |
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| 275 | |
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| 276 | if self.cmd() == '': |
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| 277 | # find the mpirun command |
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| 278 | mpiCommand = getCommandOutput('which mpirun') |
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| 279 | if mpiCommand == '': |
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| 280 | # command not found? |
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| 281 | error = 'mpirun command not found' |
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| 282 | raise RpQueueError, error |
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| 283 | else : |
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| 284 | mpiCommand = mpiCommand.strip() |
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| 285 | |
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| 286 | # check to make sure user specified an executable |
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| 287 | if self._queue_vars['executable'] == '': |
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| 288 | error = 'executable not set within pbs queue' |
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| 289 | raise RpQueueError, error |
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| 290 | |
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| 291 | self.cmd('%s -np %d -machinefile $PBS_NODEFILE %s %s' % \ |
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| 292 | (mpiCommand, self.nodes(), self.executable(), self.execArgs())) |
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| 293 | |
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| 294 | return """#PBS -S /bin/bash |
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| 295 | #PBS -l nodes=%s:ppn=%s |
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| 296 | #PBS -l walltime=%s |
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| 297 | #PBS -q %s |
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| 298 | #PBS -o %s |
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| 299 | #PBS -e %s |
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| 300 | #PBS -mn |
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| 301 | #PBS -N %s |
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| 302 | cd $PBS_O_WORKDIR |
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| 303 | |
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| 304 | cmd="%s" |
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| 305 | echo == running from $HOSTNAME: |
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| 306 | echo $cmd |
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| 307 | $cmd |
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| 308 | |
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| 309 | touch %s |
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| 310 | """ % ( self.nodes(), |
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| 311 | self.ppn(), |
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| 312 | self.walltime(), |
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| 313 | self.queue(), |
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| 314 | self.outFile(), |
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| 315 | self.errFile(), |
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| 316 | self.jobName(), |
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| 317 | self.cmd(), |
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| 318 | self.errFile() ) |
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| 319 | |
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| 320 | def cmd(self,cmd=''): |
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| 321 | cmd = str(cmd) |
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| 322 | if (cmd == 'None') or (cmd == ''): |
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| 323 | return self._pbs_vars['cmd'] |
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| 324 | else : |
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| 325 | self._pbs_vars['cmd'] = cmd |
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| 326 | |
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| 327 | def getCurrentStatus(self): |
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| 328 | retVal = self._pbs_msgs['DEFAULT'] |
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| 329 | if self._jobId: |
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| 330 | nanoHUBQ = self.queue() |
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| 331 | if nanoHUBQ != "": |
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| 332 | atLocation = nanoHUBQ.find('@') |
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| 333 | if atLocation > -1: |
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| 334 | pbsServer = nanoHUBQ[atLocation+1:] |
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| 335 | |
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| 336 | if pbsServer == '': |
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| 337 | cmd = "qstat -a | grep \'^ *%s\'" % (self._jobId) |
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| 338 | else: |
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| 339 | cmd = "qstat @%s -a | grep \'^ *%s\'" % (pbsServer,self._jobId) |
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| 340 | cmdOutput = getCommandOutput(cmd) |
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| 341 | |
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| 342 | # parse a string that should look like this: |
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| 343 | # 32049.hamlet.rc kearneyd ncn run.21557. 6104 8 8 -- 24:00 R 00:00 |
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| 344 | parseResults = cmdOutput.split() # re.compile(r'\W+').split(cmdOutput) |
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| 345 | # results should look like this: |
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| 346 | # ['32049.hamlet.rc','kearneyd','ncn','run.21557.','6104','8','8','--','24:00','R','00:00'] |
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| 347 | |
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| 348 | if len(parseResults) > 9: |
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| 349 | qstat = parseResults[9] |
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| 350 | retVal = self._pbs_msgs[qstat] |
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| 351 | |
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| 352 | return '('+self._jobId+') '+retVal |
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| 353 | |
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| 354 | def submit(self): |
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| 355 | submitFileData = self.__makePbsScript__() |
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| 356 | submitFileName = self._resultDirPath+'/'+self.jobName()+'.pbs' |
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| 357 | writeFile(submitFileName,submitFileData) |
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| 358 | |
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| 359 | myCWD = os.getcwd() |
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| 360 | os.chdir(self._resultDirPath) |
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| 361 | cmdOutData = getCommandOutput('qsub %s' % (submitFileName)) |
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| 362 | os.chdir(myCWD) |
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| 363 | |
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| 364 | self._prevStatus = '' |
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| 365 | self._currStatus = '' |
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| 366 | |
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| 367 | # a successful submission (on hamlet/lear) follows this regexp |
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| 368 | if re.match(r'[0-9]+',cmdOutData): |
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| 369 | self._jobId = re.search(r'[0-9]+',cmdOutData).group() |
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| 370 | else: |
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| 371 | error = 'Submission to PBS Queue Failed' |
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| 372 | raise RpQueueError, error |
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| 373 | |
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| 374 | # def status(self): |
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| 375 | # min = 0 |
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| 376 | # tCount = 0 |
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| 377 | # sleepTime = 10 |
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| 378 | # |
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| 379 | # while self.__checkFiles__(self.errFile()): |
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| 380 | # if tCount == 60 : |
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| 381 | # min += 1 |
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| 382 | # tCount = 0 |
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| 383 | # |
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| 384 | # self._currStatus = self.getCurrentStatus() |
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| 385 | # if (self._currStatus != self._prevStatus): |
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| 386 | # sys.stdout.write("%s: %s\n" % ( self._currStatus, time.ctime() ) ) |
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| 387 | # sys.stdout.flush() |
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| 388 | # self._prevStatus = self._currStatus |
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| 389 | # |
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| 390 | # time.sleep(sleepTime) |
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| 391 | # tCount += sleepTime |
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| 392 | |
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| 393 | |
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| 394 | |
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| 395 | class condor (queue): |
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| 396 | |
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| 397 | USE_MPI = 1 |
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| 398 | |
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| 399 | def __init__( self, |
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| 400 | jobName, |
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| 401 | resultsDir, |
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| 402 | nodes, |
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| 403 | executable, |
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| 404 | ppn=2, |
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| 405 | execArgs='', |
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| 406 | walltime='00:01:00', |
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| 407 | transferFiles=[], |
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| 408 | flags=0 ): |
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| 409 | |
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| 410 | # call the base class's init |
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| 411 | for base in self.__class__.__bases__: |
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| 412 | callbase(self, base) |
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| 413 | |
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| 414 | self._condor_msgs = {} |
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| 415 | self.__fillStatusDict__() |
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| 416 | |
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| 417 | self._flags = flags |
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| 418 | self.__setWorkingDir__() |
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| 419 | |
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| 420 | # setup the empty process lists |
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| 421 | self._processList = [] |
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| 422 | |
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| 423 | # set vars based on user input |
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| 424 | self.resultsDir(resultsDir) |
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| 425 | self.jobName(jobName) |
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| 426 | self.nodes(nodes) |
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| 427 | self.ppn(ppn) |
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| 428 | self.walltime(walltime) |
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| 429 | self.executable(executable) |
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| 430 | self.execArgs(execArgs) |
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| 431 | self.queue("tg_workq@lear") |
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| 432 | self.outFile("out.$(cluster).$(process)") |
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| 433 | self.errFile("err.$(cluster).$(process)") |
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| 434 | self.logFile("log.$(cluster)") |
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| 435 | self.transferFiles(transferFiles) |
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| 436 | |
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| 437 | def __fillStatusDict__(self): |
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| 438 | self._condor_msgs['I'] = 'Simulation Queued' |
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| 439 | self._condor_msgs['H'] = 'Simulation Held' |
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| 440 | self._condor_msgs['R'] = 'Running Simulation' |
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| 441 | self._condor_msgs['C'] = 'Simulation Complete' |
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| 442 | self._condor_msgs['X'] = 'Simulation Marked For Deletion' |
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| 443 | self._condor_msgs['DEFAULT'] = 'Returning Results...' |
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| 444 | |
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| 445 | def __setWorkingDir__(self): |
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| 446 | session = os.getenv("SESSION","00000X") |
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| 447 | epoch = int(time.mktime(datetime.datetime.utcnow().timetuple())) |
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| 448 | self._workingdir = str(epoch) + "_" + session |
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| 449 | |
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| 450 | def __makeCondorScript__(self): |
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| 451 | # return """universe=grid |
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| 452 | # gridresource = gt2 tg-gatekeeper.purdue.teragrid.org:2120/jobmanager-pbs |
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| 453 | # executable = EXECUTABLE |
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| 454 | # output = out.$(cluster).$(process) |
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| 455 | # error = err.$(cluster).$(process) |
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| 456 | # should_transfer_files = YES |
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| 457 | # when_to_transfer_output = ON_EXIT |
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| 458 | # initialDir = MY_RESULT_DIR |
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| 459 | # log = log.$(cluster) |
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| 460 | # #globusrsl = (project=TG-ECD060000N)(jobType=mpi)(count=2)(hostcount=2)(maxWallTime=WALLTIME) |
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| 461 | # globusrsl = (project=TG-ECD060000N)(maxWallTime=WALLTIME)MPIRSL(queue=tg_workq@lear) |
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| 462 | # notification = never |
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| 463 | # """ |
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| 464 | |
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| 465 | self._resultDirPath = os.path.join(os.getcwd(),self.resultsDir()) |
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| 466 | |
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| 467 | self._mpirsl = "" |
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| 468 | if (self._flags & self.USE_MPI): |
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| 469 | # host_xcount is the number of machines |
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| 470 | # xcount is the number of procs per machine |
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| 471 | self._mpirsl = "(jobType=mpi)(xcount=%d)(host_xcount=%d)" % \ |
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| 472 | (self.ppn(), self.nodes()) |
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| 473 | |
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| 474 | (wall_hr,wall_min,wall_sec) = self.walltime().split(":") |
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| 475 | walltime = int(wall_hr)*60 + int(wall_min) + int(wall_sec)/60.00 |
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| 476 | |
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| 477 | return """universe=grid |
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| 478 | gridresource = gt2 tg-gatekeeper.purdue.teragrid.org/jobmanager-pbs |
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| 479 | executable = %s |
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| 480 | output = %s |
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| 481 | error = %s |
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| 482 | should_transfer_files = YES |
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| 483 | when_to_transfer_output = ON_EXIT |
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| 484 | initialDir = %s |
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| 485 | log = %s |
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| 486 | #globusrsl = (project=TG-ECD060000N)(jobType=mpi)(xcount=2)(hostxcount=2)(maxWallTime=WALLTIME) |
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| 487 | globusrsl = (project=TG-ECD060000N)(maxWallTime=%g)%s(queue=%s) |
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| 488 | notification = never |
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| 489 | """ % ( self.executable(), |
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| 490 | self.outFile(), |
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| 491 | self.errFile(), |
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| 492 | self.resultsDir(), |
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| 493 | self.logFile(), |
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| 494 | walltime, |
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| 495 | self._mpirsl, |
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| 496 | self.queue() ) |
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| 497 | |
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| 498 | def addProcess(self,argsList=[],inputFiles=[]): |
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| 499 | # return """arguments = ARGUMENT resultsID.tar.gz WORKINGDIR_ID |
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| 500 | # transfer_input_files = INFILE,\\ |
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| 501 | # APPROOT/grid.1.poly,\\ |
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| 502 | # APPROOT/grid.1.node,\\ |
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| 503 | # APPROOT/grid.1.ele,\\ |
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| 504 | # APPROOT/grid.1.edge |
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| 505 | # transfer_output_files = resultsID.tar.gz |
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| 506 | # Queue |
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| 507 | # """ |
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| 508 | args = " ".join(argsList) |
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| 509 | transInFiles = ",\\\\\n\t\t".join(inputFiles) |
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| 510 | nextProcId = len(self._processList) |
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| 511 | resultsTarName = "%s%d.tar.gz" % (self.jobName(),nextProcId) |
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| 512 | newProcess = """arguments = %s %s %s_%d |
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| 513 | transfer_input_files = %s |
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| 514 | transfer_output_files = %s |
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| 515 | Queue |
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| 516 | |
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| 517 | """ % ( args, |
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| 518 | resultsTarName, |
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| 519 | self._workingdir, |
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| 520 | nextProcId, |
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| 521 | transInFiles, |
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| 522 | resultsTarName ) |
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| 523 | self._processList.append(newProcess) |
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| 524 | |
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| 525 | |
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| 526 | def getCurrentStatus(self): |
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| 527 | if self._jobId: |
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| 528 | chkCmd = "condor_q | grep \'^ *%s\'" % (self._jobId) |
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| 529 | cmdOutput = getCommandOutput(chkCmd) |
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| 530 | |
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| 531 | # parse a string that should look like this: |
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| 532 | # 61.0 dkearney 12/9 22:47 0+00:00:00 I 0 0.0 nanowire.sh input- |
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| 533 | |
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| 534 | parseResults = cmdOutput.split() # re.compile(r'\W+').split(cmdOutput) |
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| 535 | |
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| 536 | # results should look like this: |
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| 537 | # ['61.0', 'dkearney', '12/9', '22:47', '0+00:00:00', 'I', '0', '0.0', 'nanowire.sh', 'input-'] |
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| 538 | |
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| 539 | retVal = '' |
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| 540 | |
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| 541 | if len(parseResults) > 6: |
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| 542 | qstat = parseResults[5] |
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| 543 | retVal = self._condor_msgs[qstat] |
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| 544 | |
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| 545 | if retVal == '': |
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| 546 | retVal = self._condor_msgs['DEFAULT'] |
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| 547 | |
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| 548 | return retVal |
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| 549 | |
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| 550 | def __checkFiles__(self): |
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| 551 | numJobs = len(self._processList) |
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| 552 | retVal = numJobs |
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| 553 | for i in xrange(numJobs): |
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| 554 | resultTarPath = self.resultsDir() + "/" + self.jobName() + str(i) + ".tar.gz" |
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| 555 | |
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| 556 | # this might be the point of a race condition, |
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| 557 | # might need to change this to a try/catch statement. |
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| 558 | # check to see that the result file exists, if not raise error |
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| 559 | if (not os.path.exists(resultTarPath)): |
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| 560 | error = 'Condor Result file not created: %s' % (resultTarPath) |
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| 561 | raise RuntimeError, error |
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| 562 | sys.exit(-1) |
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| 563 | |
|---|
| 564 | # check to see that the result tar size is greater than 0 |
|---|
| 565 | resultTarSize = os.path.getsize(resultTarPath) |
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| 566 | if (resultTarSize): |
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| 567 | retVal -= 1 |
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| 568 | |
|---|
| 569 | return retVal |
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| 570 | |
|---|
| 571 | def status(self): |
|---|
| 572 | min = 0 |
|---|
| 573 | tCount = 0 |
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| 574 | sleepTime = 10 |
|---|
| 575 | |
|---|
| 576 | while self.__checkFiles__(): |
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| 577 | if tCount == 60 : |
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| 578 | min += 1 |
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| 579 | tCount = 0 |
|---|
| 580 | |
|---|
| 581 | self._currStatus = self.getCurrentStatus() |
|---|
| 582 | if (self._currStatus != self._prevStatus): |
|---|
| 583 | sys.stdout.write("%s: %s\n" % ( self._currStatus, time.ctime() ) ) |
|---|
| 584 | sys.stdout.flush() |
|---|
| 585 | self._prevStatus = self._currStatus |
|---|
| 586 | |
|---|
| 587 | time.sleep(sleepTime) |
|---|
| 588 | tCount += sleepTime |
|---|
| 589 | |
|---|
| 590 | def submit(self): |
|---|
| 591 | |
|---|
| 592 | if len(self._processList) == 0: |
|---|
| 593 | self.addProcess(inputFiles=self.transferFiles()) |
|---|
| 594 | |
|---|
| 595 | submitFileData = self.__makeCondorScript__() + "\n".join(self._processList) |
|---|
| 596 | submitFileName = self._resultDirPath+'/'+self.jobName()+'.condor' |
|---|
| 597 | writeFile(submitFileName,submitFileData) |
|---|
| 598 | |
|---|
| 599 | # submit the condor job |
|---|
| 600 | myCWD = os.getcwd() |
|---|
| 601 | os.chdir(self._resultDirPath) |
|---|
| 602 | condorCmd = 'condor_submit %s 2> condor_submit.error' % (submitFileName) |
|---|
| 603 | cmdOutData = getCommandOutput(condorCmd) |
|---|
| 604 | os.chdir(myCWD) |
|---|
| 605 | |
|---|
| 606 | self._prevStatus = '' |
|---|
| 607 | self._currStatus = '' |
|---|
| 608 | |
|---|
| 609 | # a successful submission (on hamlet/lear) follows this regexp |
|---|
| 610 | if re.search(r'cluster ([0-9]+)',cmdOutData): |
|---|
| 611 | self._jobId = re.search(r'cluster ([0-9]+)',cmdOutData).group(1) |
|---|
| 612 | else: |
|---|
| 613 | print "cmdOutData returned :%s:" % cmdOutData |
|---|
| 614 | error = 'Submission to Condor Queue Failed' |
|---|
| 615 | # raise RpQueueError, error |
|---|
| 616 | |
|---|
| 617 | ####################################################################### |
|---|
| 618 | # main python script |
|---|
| 619 | ####################################################################### |
|---|
| 620 | |
|---|
| 621 | ####################################################################### |
|---|
| 622 | |
|---|
| 623 | def createDir(dirName): |
|---|
| 624 | resultDirPath = os.getcwd() + "/" + dirName |
|---|
| 625 | if os.path.exists(resultDirPath): |
|---|
| 626 | shutil.rmtree(resultDirPath) |
|---|
| 627 | os.mkdir(resultDirPath) |
|---|
| 628 | return resultDirPath |
|---|
| 629 | |
|---|
| 630 | if __name__ == '__main__': |
|---|
| 631 | |
|---|
| 632 | nodes = 5 |
|---|
| 633 | walltime = '01:00:00' |
|---|
| 634 | mpiCommand = getCommandOutput('which mpirun') |
|---|
| 635 | |
|---|
| 636 | if mpiCommand == '': |
|---|
| 637 | # command not found? |
|---|
| 638 | sys.exit(-1) |
|---|
| 639 | else : |
|---|
| 640 | mpiCommand = mpiCommand.strip() |
|---|
| 641 | |
|---|
| 642 | sys.stdout.write("testing hello with condor\n") |
|---|
| 643 | jobName = 'helloMPITest' |
|---|
| 644 | resultsDir = createDir('4321') |
|---|
| 645 | executable = './hello.sh' |
|---|
| 646 | txFileList = ['hello'] |
|---|
| 647 | shutil.copy('hello/hello.sh',resultsDir) |
|---|
| 648 | shutil.copy('hello/hello',resultsDir) |
|---|
| 649 | myCondorObj = condor(jobName,resultsDir,2,executable,ppn=1,walltime=walltime,transferFiles=txFileList,flags=condor.USE_MPI) |
|---|
| 650 | myCondorObj.submit() |
|---|
| 651 | myCondorObj.status() |
|---|
| 652 | sys.stdout.flush() |
|---|
| 653 | |
|---|
| 654 | sys.stdout.write("testing hello\n") |
|---|
| 655 | jobName = 'helloRP_MPITest' |
|---|
| 656 | resultsDir = createDir('abab') |
|---|
| 657 | executable = 'helloRP' |
|---|
| 658 | driver = "driver7878.xml" |
|---|
| 659 | shutil.copy('hello/helloRP',resultsDir) |
|---|
| 660 | shutil.copy(driver,resultsDir) |
|---|
| 661 | myPBSObj = pbs(jobName,resultsDir,nodes,executable,driver) |
|---|
| 662 | myPBSObj.submit() |
|---|
| 663 | myPBSObj.status() |
|---|
| 664 | sys.stdout.flush() |
|---|
| 665 | |
|---|
| 666 | |
|---|
| 667 | sys.stdout.write("testing hello\n") |
|---|
| 668 | jobName = 'helloMPITest' |
|---|
| 669 | resultsDir = createDir('1234') |
|---|
| 670 | executable = 'hello' |
|---|
| 671 | shutil.copy('hello/hello',resultsDir) |
|---|
| 672 | myPBSObj = pbs(jobName,resultsDir,nodes,executable) |
|---|
| 673 | myPBSObj.submit() |
|---|
| 674 | myPBSObj.status() |
|---|
| 675 | sys.stdout.flush() |
|---|
| 676 | |
|---|
| 677 | sys.stdout.write("testing cycle\n") |
|---|
| 678 | jobName = 'cycleMPITest' |
|---|
| 679 | resultsDir = createDir('5678') |
|---|
| 680 | cmd = '%s -np %d -machinefile $PBS_NODEFILE cycle' % (mpiCommand,nodes) |
|---|
| 681 | shutil.copy('cycle/cycle',resultsDir) |
|---|
| 682 | myPBSObj = pbs(jobName,resultsDir,nodes,"") |
|---|
| 683 | myPBSObj.cmd(cmd) |
|---|
| 684 | myPBSObj.walltime('00:02:00') |
|---|
| 685 | myPBSObj.submit() |
|---|
| 686 | myPBSObj.status() |
|---|
| 687 | sys.stdout.flush() |
|---|
| 688 | |
|---|
| 689 | # exit the program |
|---|
| 690 | sys.exit() |
|---|
| 691 | |
|---|
| 692 | ####################################################################### |
|---|
