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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 import os
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33 import time
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34 import datetime
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35 import sys
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36 from commons.core.sql.Job import Job
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37 from commons.core.sql.TableAdaptator import TableAdaptator
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38
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39 ## Methods for Job persistence
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40 #
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41 class TableJobAdaptator(TableAdaptator):
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42
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43 ## Record a job
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44 #
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45 # @param job Job instance with the job informations
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46 #
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47 def recordJob(self, job):
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48 self.removeJob(job)
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49 sqlCmd = "INSERT INTO %s" % self._table
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50 sqlCmd += " VALUES ("
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51 sqlCmd += " \"%s\"," % job.jobid
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52 sqlCmd += " \"%s\"," % job.jobname
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53 sqlCmd += " \"%s\"," % job.groupid
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54 sqlCmd += " \"%s\"," % job.launcher
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55 sqlCmd += " \"%s\"," % job.queue
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56 sqlCmd += " \"%s\"," % job.lResources
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57 sqlCmd += " \"waiting\","
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58 sqlCmd += " \"%s\"," % time.strftime("%Y-%m-%d %H:%M:%S")
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59 sqlCmd += " \"?\" );"
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60 self._iDb.execute(sqlCmd)
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61
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62
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63 ## Remove a job from the job table
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64 #
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65 # @param job: job instance to remove
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66 #
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67 def removeJob(self, job):
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68 qry = "DELETE FROM %s" % self._table
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69 qry += " WHERE groupid='%s'" % job.groupid
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70 qry += " AND jobname='%s'" % job.jobname
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71 qry += " AND launcher='%s';" % job.launcher
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72 self._iDb.execute(qry)
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73
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74
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75 ## Set the jobid of a job with the id of SGE
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76 #
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77 # @param job job instance
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78 # @param jobid integer
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79 #
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80 def updateJobIdInDB(self, job, jobid):
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81 #TODO: check if only one job will be updated
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82 qry = "UPDATE %s" % self._table
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83 qry += " SET jobid='%i'" % int(jobid)
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84 qry += " WHERE jobname='%s'" % job.jobname
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85 qry += " AND groupid='%s'" % job.groupid
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86 qry += " AND launcher='%s';" % job.launcher
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87 self._iDb.execute(qry)
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88
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89
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90 ## Get a job status
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91 #
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92 # @param job: a Job instance with the job informations
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93 #
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94 def getJobStatus(self, job):
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95 if job.jobid != 0 and job.jobname == "":
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96 job.jobname = job.jobid
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97 job.jobid = 0
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98 qry = "SELECT status FROM %s" % self._table
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99 qry += " WHERE groupid='%s'" % job.groupid
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100 qry += " AND jobname='%s'" % job.jobname
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101 qry += " AND launcher='%s';" % job.launcher
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102 self._iDb.execute(qry)
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103 res = self._iDb.fetchall()
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104 if len(res) > 1:
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105 sys.stderr.write("ERROR while getting job status: non-unique jobs\n")
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106 sys.stderr.flush()
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107 sys.exit(1)
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108 if res == None or len(res) == 0:
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109 return "unknown"
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110 return res[0][0]
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111
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112
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113 ## Change a job status
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114 #
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115 # @param job: a Job instance with the job informations
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116 # @param status: the new status (waiting,finished,error)
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117 #
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118 def changeJobStatus(self, job, status):
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119 sqlCmd = "UPDATE %s" % self._table
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120 sqlCmd += " SET status='%s'" % status
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121 sqlCmd += ", node='%s'" % job.node
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122 sqlCmd += " WHERE groupid='%s'" % job.groupid
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123 sqlCmd += " AND jobname='%s'" % job.jobname
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124 sqlCmd += " AND launcher='%s';" % job.launcher
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125 self._iDb.execute(sqlCmd)
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126
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127
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128 ## Get the number of jobs belonging to the desired groupid with the desired status.
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129 #
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130 # @param groupid string a group identifier to record related job series
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131 # @param status string job status (waiting, running, finished, error)
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132 # @return int
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133 #
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134 def getCountStatus(self, groupid, status):
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135 qry = "SELECT count(jobname) FROM %s" % self._table
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136 qry += " WHERE groupid='%s'" % groupid
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137 qry += " AND status='%s';" % status
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138 self._iDb.execute(qry)
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139 res = self._iDb.fetchall()
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140 return int(res[0][0])
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141
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142
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143 ## Clean all job from a job group
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144 #
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145 # @param groupid: a group identifier to record related job series
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146 #
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147 def cleanJobGroup(self, groupid):
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148 qry = "DELETE FROM %s WHERE groupid='%s';" % (self._table, groupid)
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149 self._iDb.execute(qry)
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150
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151
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152 ## Check if there is unfinished job from a job group.
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153 #
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154 # @param groupid string a group identifier to record related job series
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155 #
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156 def hasUnfinishedJob(self, groupid):
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157 qry = "SELECT * FROM %s" % self._table
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158 qry += " WHERE groupid='%s'" % groupid
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159 qry += " and status!='finished';"
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160 self._iDb.execute(qry)
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161 res = self._iDb.fetchall()
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162 if len(res) == 0:
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163 return False
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164 return True
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165
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166
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167 ## Wait job finished status from a job group.
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168 # Job are re-launched if error (max. 3 times)
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169 #
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170 # @param groupid string a group identifier to record related job series
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171 # @param checkInterval integer time laps in seconds between two checks (default = 5)
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172 # @param maxRelaunch integer max nb of times a job in error is relaunch before exiting (default = 3)
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173 # @param exitIfTooManyErrors boolean exit if a job is still in error above maxRelaunch (default = True)
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174 # @param timeOutPerJob integer max nb of seconds after which one tests if a job is still in SGE or not (default = 60*60=1h)
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175 #
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176 def waitJobGroup(self, groupid, checkInterval=5, maxRelaunch=3, exitIfTooManyErrors=True, timeOutPerJob=60*60):
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177 dJob2Err = {}
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178
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179 # retrieve the total number of jobs belonging to the desired groupid
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180 qry = "SELECT count(jobname) FROM %s WHERE groupid='%s';" % (self._table, groupid)
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181 self._iDb.execute(qry)
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182 totalNbJobs = int(self._iDb.fetchall()[0][0])
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183
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184 nbTimeOuts = 0
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185
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186 while True:
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187 time.sleep(checkInterval)
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188 # retrieve the finished jobs and stop if all jobs are finished
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189 nbFinishedJobs = self.getCountStatus(groupid, "finished")
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190 if nbFinishedJobs == totalNbJobs:
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191 break
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192
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193 # retrieve the jobs in error and relaunch them if they are in error (max. 'maxRelaunch' times)
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194 qry = "SELECT * FROM %s" % self._table
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195 qry += " WHERE groupid='%s'" % groupid
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196 qry += " AND status ='error';"
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197 self._iDb.execute(qry)
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198 lJobsInError = self._iDb.fetchall()
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199 for job in lJobsInError:
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200 jobName = job[1]
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201 if not dJob2Err.has_key(jobName):
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202 dJob2Err[jobName] = 1
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203 if dJob2Err[jobName] < maxRelaunch:
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204 print "job '%s' in error, re-submitting (%i)" % (job[1], dJob2Err[job[1]])
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205 sys.stdout.flush()
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206 lResources = job[5].replace("[", "").replace("]", "").replace("'", "").split(", ")
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207 newJob = Job(jobname=jobName, groupid=job[2], launcherFile=job[3], queue=job[4], lResources=lResources)
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208 self.submitJob(newJob)
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209 dJob2Err[jobName] += 1
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210 else:
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211 dJob2Err[jobName] += 1
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212 cmd = "job '%s' in permanent error (>%i)" % (jobName, maxRelaunch)
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213 cmd += "\ngroupid = %s" % groupid
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214 cmd += "\nnb of jobs = %i" % totalNbJobs
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215 cmd += "\nnb of finished jobs = %i" % self.getCountStatus(groupid, "finished")
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216 cmd += "\nnb of waiting jobs = %i" % self.getCountStatus(groupid, "waiting")
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217 cmd += "\nnb of running jobs = %i" % self.getCountStatus(groupid, "running")
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218 cmd += "\nnb of jobs in error = %i" % self.getCountStatus(groupid, "error")
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219 sys.stdout.flush()
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220 if exitIfTooManyErrors:
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221 self.cleanJobGroup(groupid)
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222 sys.exit(1)
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223 else:
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224 checkInterval = 60
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225 nbTimeOuts = self._checkIfJobsTableAndJobsManagerInfoAreConsistent(nbTimeOuts, timeOutPerJob, groupid)
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226
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227
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228 ## Submit a job to a queue and record it in job table.
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229 #
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230 # @param job a job instance
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231 # @param maxNbWaitingJobs integer max nb of waiting jobs before submitting a new one (default = 10000)
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232 # @param checkInterval integer time laps in seconds between two checks (default = 30)
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233 # @param verbose integer (default = 0)
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234 #
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235 def submitJob(self, job, verbose=0, maxNbWaitingJobs=10000, checkInterval=30):
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236 if self.getJobStatus(job) in ["waiting", "running", "finished"]:
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237 sys.stderr.write( "WARNING: job '%s' was already submitted\n" % job.jobname)
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238 sys.stderr.flush()
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239 self.cleanJobGroup(job.groupid)
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240 sys.exit(1)
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241
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242 while self.getCountStatus(job.groupid, "waiting") > maxNbWaitingJobs:
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243 time.sleep(checkInterval)
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244
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245 self.recordJob(job)
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246 cmd = self._getQsubCommand(job)
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247 returnStatus = os.system(cmd)
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248
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249 if returnStatus == 0:
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250 fileName = "jobid.stdout"
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251 jobidFileHandler = open(fileName, "r")
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252 jobid = self._getJobidFromJobManager(jobidFileHandler)
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253 if verbose > 0:
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254 print "job '%i %s' submitted" % (jobid, job.jobname)
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255 sys.stdout.flush()
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256 job.jobid = jobid
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257 jobidFileHandler.close()
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258 self.updateJobIdInDB(job, jobid)
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259 os.remove(fileName)
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260 return returnStatus
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261
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262
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263 ## Get the list of nodes where jobs of one group were executed
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264 #
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265 # @param groupid string a group identifier of job series
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266 # @return lNodes list of nodes names without redundancy
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267 #
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268 def getNodesListByGroupId(self, groupId):
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269 qry = "SELECT DISTINCT node FROM %s" % self._table
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270 qry += " WHERE groupid='%s'" % groupId
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271 self._iDb.execute(qry)
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272 res = self._iDb.fetchall()
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273 lNodes = []
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274 for resTuple in res:
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275 lNodes.append(resTuple[0])
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276 return lNodes
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277
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278 def checkJobTable(self):
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279 if not self._iDb.doesTableExist(self._table):
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280 self._iDb.createTable(self._table, "jobs")
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281 else:
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282 lExpFields = sorted(["jobid", "jobname", "groupid", "launcher", "queue", "resources", "status", "time", "node"])
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283 lObsFields = sorted(self._iDb.getFieldList(self._table))
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284 if lExpFields != lObsFields:
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285 self._iDb.createTable(self._table, "jobs", overwrite = True)
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286
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287 def close(self):
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288 self._iDb.close()
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289
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290 def _getJobidAndNbJob(self, jobid) :
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291 tab = jobid.split(".")
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292 jobid = tab[0]
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293 tab = tab[1].split(":")
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294 nbJob = tab[0]
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295 return jobid, nbJob
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296
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297 class TableJobAdaptatorSGE(TableJobAdaptator):
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298
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299 def _checkIfJobsTableAndJobsManagerInfoAreConsistent(self, nbTimeOuts, timeOutPerJob, groupid):
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300 # retrieve the date and time at which the oldest, still-running job was submitted
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301 sql = "SELECT jobid,jobname,time FROM %s WHERE groupid='%s' AND status='running' ORDER BY time DESC LIMIT 1" % (self._table, groupid)
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302 self._iDb.execute( sql )
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303 res = self._iDb.fetchall()
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304 if len(res) > 0:
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305 jobid = res[0][0]
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306 jobname = res[0][1]
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307 dateTimeOldestJob = res[0][2]
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308 dateTimeCurrent = datetime.datetime.now()
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309 # delta is time between (i) first job launched of the given groupid and still in running state and (ii) current time
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310 delta = dateTimeCurrent - dateTimeOldestJob
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311 # check if delta is in an interval: 0 <= delta < 1h | 1h <= delta < 2h | 2h <= delta < 3h (timeOutPerJob = 1h)
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312 if delta.seconds >= nbTimeOuts * timeOutPerJob and delta.seconds < (nbTimeOuts+1) * timeOutPerJob:
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313 return nbTimeOuts
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314 # delta outside the interval: go to next interval (time out)
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315 if delta.seconds >= (nbTimeOuts+1) * timeOutPerJob:
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316 nbTimeOuts += 1
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317 # Job with 'running' status should be in qstat. Because status in DB is set at 'running' by the job launched.
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318 if not self.isJobStillHandledBySge(jobid, jobname):
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319 # But if not, let time for the status update (in DB), if the job finished between the query execution and now.
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320 time.sleep( 5 )
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321 # If no update at 'finished', exit
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322 #TODO: check status in DB
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323 if not self.isJobStillHandledBySge(jobid, jobname):
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324 msg = "ERROR: job '%s', supposedly still running, is not handled by SGE anymore" % ( jobid )
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325 msg += "\nit was launched the %s (> %.2f hours ago)" % ( dateTimeOldestJob, timeOutPerJob/3600.0 )
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326 msg += "\nthis problem can be due to:"
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327 msg += "\n* memory shortage, in that case, decrease the size of your jobs;"
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328 msg += "\n* timeout, in that case, decrease the size of your jobs;"
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329 msg += "\n* node failure or database error, in that case, launch the program again or ask your system administrator."
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330 sys.stderr.write("%s\n" % msg)
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331 sys.stderr.flush()
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332 self.cleanJobGroup(groupid)
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333 sys.exit(1)
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334 return nbTimeOuts
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335
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336 ## Check if a job is still handled by SGE
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337 #
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338 # @param jobid string job identifier
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339 # @param jobname string job name
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340 #
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341 def isJobStillHandledBySge(self, jobid, jobname):
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342 isJobInQstat = False
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343 qstatFile = "qstat_stdout"
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344 cmd = "qstat > %s" % qstatFile
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345 returnStatus = os.system(cmd)
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346 if returnStatus != 0:
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347 msg = "ERROR while launching 'qstat'"
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348 sys.stderr.write( "%s\n" % msg )
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349 sys.exit(1)
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350 qstatFileHandler = open(qstatFile, "r")
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351 lLines = qstatFileHandler.readlines()
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352 for line in lLines:
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353 tokens = line.split()
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354 if len(tokens) > 3 and tokens[0] == str(jobid) and tokens[2] == jobname[0:len(tokens[2])]:
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355 isJobInQstat = True
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356 break
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357 qstatFileHandler.close()
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358 os.remove(qstatFile)
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359 return isJobInQstat
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360
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361 def _getQsubCommand(self, job):
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362 cmd = "echo '%s' | " % job.launcher
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363 prg = "qsub"
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364 cmd += prg
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365 cmd += " -V"
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366 cmd += " -N %s" % job.jobname
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367 if job.queue != "":
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368 cmd += " -q %s" % job.queue
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369 cmd += " -cwd"
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370 if job.lResources != []:
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371 cmd += " -l \""
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372 cmd += " ".join(job.lResources)
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373 cmd += "\""
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374 if job.parallelEnvironment != "":
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375 cmd += " -pe " + job.parallelEnvironment
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376 cmd += " > jobid.stdout"
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377 return cmd
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378
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379 def _getJobidFromJobManager(self, jobidFileHandler):
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380 return int(jobidFileHandler.readline().split(" ")[2])
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381
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382
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383 class TableJobAdaptatorTorque(TableJobAdaptator):
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384
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385 def _checkIfJobsTableAndJobsManagerInfoAreConsistent(self, nbTimeOuts, timeOutPerJob, groupid):
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386 return nbTimeOuts
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387
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388 def _getQsubCommand(self, job):
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389 cmd = "echo '%s' | " % job.launcher
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390 prg = "qsub"
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391 cmd += prg
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392 cmd += " -V"
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393 cmd += " -d %s" % os.getcwd()
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394 cmd += " -N %s" % job.jobname
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395 if job.queue != "":
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396 cmd += " -q %s" % job.queue
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397 if job.lResources != []:
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398 cmd += " -l \""
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399 cmd += " ".join(job.lResources).replace("mem_free","mem")
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400 cmd += "\""
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401 cmd += " > jobid.stdout"
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402 return cmd
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403
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404 def _getJobidFromJobManager(self, jobidFileHandler):
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405 return int(jobidFileHandler.readline().split(".")[0])
|
