| 1 | #!/bin/bash
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| 2 | #
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| 3 | # This a script, which launches other scripts (all scripts, that are run
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| 4 | # on primary basis)
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| 5 | #
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| 6 |
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| 7 | source `dirname $0`/../Sourcefile.sh
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| 8 | printprocesslog "INFO starting $0"
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| 9 |
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| 10 | set -C
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| 11 | shopt -s expand_aliases
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| 12 |
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| 13 | # function to continue in loop and go to next script
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| 14 | function sleepawhile()
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| 15 | {
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| 16 | usedsleeptime=$sleeptime
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| 17 | case $1 in
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| 18 | "error") if ! [ "$errorsleeptime" = "" ]
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| 19 | then
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| 20 | if [ $errorsleeptime -lt $sleeptimelimit ]
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| 21 | then
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| 22 | errorsleeptime=`echo " $errorsleeptime + $errorsleeptimedefault " | bc`
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| 23 | fi
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| 24 | usedsleeptime=$errorsleeptime
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| 25 | fi
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| 26 | ;;
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| 27 | "ok") errorsleeptime=$errorsleeptimedefault
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| 28 | ;;
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| 29 | esac
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| 30 | echo `date +%F\ %T`" sleeping "$usedsleeptime" seconds... (status: "$1")" >> $jmscriptlog 2>&1
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| 31 | echo "" >> $jmscriptlog 2>&1
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| 32 | sleep $usedsleeptime
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| 33 | continue
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| 34 | }
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| 35 |
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| 36 | echo "" >> $jmscriptlog 2>&1
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| 37 | echo "" >> $jmscriptlog 2>&1
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| 38 | echo -n `date +%F\ %T`" starting jobmanager for setup "$AUTOMATIONSETUP >> $jmscriptlog 2>&1
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| 39 |
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| 40 | user=`whoami`
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| 41 |
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| 42 | # choose commands according to queueing system (defined in setup)
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| 43 | case $queuesys in
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| 44 | sge) echo " on queuing system 'sun grid engine'" >> $jmscriptlog 2>&1
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| 45 | # (-hard) -l hostname=compute-*
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| 46 | # for qstat this returns the jobs running on that node + all jobs in the queue
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| 47 | alias 'queuesubmit'='$sgepath/qsub -b y -q fact_long -t 1-`echo $tosubmit` -v AUTOMATIONSETUP=$AUTOMATIONSETUP -e `echo $runlogpath`/error-`echo $date`.log -o `echo $runlogpath`/log-`echo $date`.log `echo $noderequirementsub` -N `echo $step` `echo $scriptspath`/`echo ${scripts[$i]}` '
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| 48 | # alias 'queuesubmit'='$sgepath/qsub -b y -v AUTOMATIONSETUP=$AUTOMATIONSETUP -e `echo $runlogpath`/error-`echo $date`.log -o `echo $runlogpath`/log-`echo $date`.log `echo $scriptspath`/`echo ${scripts[$i]}` '
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| 49 | # alias 'queuesubmit'='$sgepath/qsub -sc runlogpath=`echo $runlogpath` -sc date=`echo $date` -sc scriptspath=`echo $scriptspath` -sc script=`echo ${scripts[$i]}` `echo $scriptspath`/job.sge '
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| 50 | # FIXME: get complete scriptname (including command line option), needed for runstereo
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| 51 | alias 'checkqueue'="$sgepath/qstat \`echo \$noderequirementstat\` | awk ' { print \"Owner\"\$4\" \" \$3\"Jobstatus\"\$5 } '"
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| 52 | #break
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| 53 | ;;
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| 54 | # pbs) echo " on queuing system 'pbs'" >> $jmscriptlog 2>&1
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| 55 | # alias 'queuesubmit'='$pbspath/qsub -t 1-`echo $tosubmit` -l walltime=`echo $walltime` -l pmem=`echo $pmem` -v AUTOMATIONSETUP=$AUTOMATIONSETUP,SOURCEFILEPATH=$SOURCEFILEPATH,SCRIPTNAME=`echo ${scripts[$i]}` -e `echo $runlogpath`/error-`echo $date`.log -o `echo $runlogpath`/log-`echo $date`.log `echo $noderequirementsub` `echo $scriptspath`/`echo ${scripts[$i]}` '
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| 56 | # # check queue (restricted to current user only)
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| 57 | # alias 'checkqueue'="$pbspath/qstat -a -u $user | awk ' { print \"Owner\"\$2\" \" \$4\"Jobstatus\"\$10 } '"
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| 58 | # #break
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| 59 | # ;;
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| 60 | # condor) echo " on queuing system 'condor'" >> $jmscriptlog 2>&1
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| 61 | # alias 'queuesubmit'='$condorpath/condor_submit -a path=`echo $scriptspath` -a prog=`echo ${scripts[$i]}` -a date=`echo $date` -a dir=`echo $runlogpath` -a num=`echo $tosubmit` -a automationsetup=$AUTOMATIONSETUP `echo $scriptspath`/run.condor'
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| 62 | # alias 'checkqueue'='$condorpath/condor_q -global -format "Owner%s " Owner -format "%s" CMD -format "Jobstatus%s\n" Jobstatus '
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| 63 | # #break
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| 64 | # ;;
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| 65 | *) echo "" >> $jmscriptlog 2>&1
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| 66 | finish >> $jmscriptlog 2>&1
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| 67 | ;;
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| 68 | esac
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| 69 |
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| 70 | echo "" >> $jmscriptlog 2>&1
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| 71 |
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| 72 | # for processing with local storage on different nodes
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| 73 | currentnode=$minnode
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| 74 | numevaluated=0
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| 75 |
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| 76 | # endless loop
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| 77 | notcount=0
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| 78 | errorsleeptime=$errorsleeptimedefault
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| 79 | while (( $notcount < 100 ))
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| 80 | do
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| 81 | # get and set some information for the processing
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| 82 | source `dirname $0`/../Sourcefile.sh
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| 83 | # reset some values
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| 84 | tosubmit=0
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| 85 | idleratio=0
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| 86 | addtoscript=
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| 87 |
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| 88 | # get processes in queue
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| 89 | q=(`checkqueue 2>&1 `)
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| 90 | if echo $q | egrep \(Error\|failed\)
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| 91 | then
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| 92 | echo `date +%F\ %T`" WARN checking query ($queuesys) failed" >> $jmscriptlog 2>&1
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| 93 | printprocesslog "WARN checking query ($queuesys) failed"
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| 94 | echo `date +%F\ %T`" WARN checking query ($queuesys) failed" >> $jmerrorlog
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| 95 | sleepawhile "error"
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| 96 | fi
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| 97 |
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| 98 | # general check whether one should submit something depending on chosen algorithm
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| 99 | # algorithm 1:
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| 100 | # submit new jobs in case there are less than $limitidle idle jobs in the queue
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| 101 | # algorithm 2:
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| 102 | # submit new jobs in case the total number of jobs in the queue has fallen below $totalpno
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| 103 | case $algorithm in
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| 104 | 1) # algorithm 1
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| 105 | # get number of idle jobs in the queue
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| 106 | q5=( `echo ${q[@]} | egrep -o \(Jobstatus1\|Jobstatusq\|JobstatusQ\)` )
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| 107 | idle=${#q5[@]}
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| 108 | if [ $idle -gt $limitidle ]
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| 109 | then
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| 110 | echo `date +%F\ %T`" more than "$limitidle" jobs waiting ("$idle")" >> $jmscriptlog 2>&1
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| 111 | sleepawhile "ok"
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| 112 | fi
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| 113 | ;;
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| 114 | 2) # algorithm 2
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| 115 | # get processes of user in queue
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| 116 | q1=( `echo ${q[@]} | egrep -o "Owner$user"`)
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| 117 | queued=${#q1[@]}
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| 118 | hour=`date +%k`
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| 119 | # choose array of total number of jobs to be done
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| 120 | # according to the day of the week
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| 121 | dayofweek=`date +%u`
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| 122 | case $dayofweek in
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| 123 | 0 | 6) totalpno=${pnototal[$hour]} ;;
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| 124 | *) totalpno=${pnototalwe[$hour]} ;;
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| 125 | esac
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| 126 | # get total number of jobs to be submitted
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| 127 | if [ $queued -gt $totalpno ]
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| 128 | then
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| 129 | echo `date +%F\ %T`" more than "$totalpno" jobs waiting ("$queued")" >> $jmscriptlog 2>&1
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| 130 | sleepawhile "ok"
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| 131 | else
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| 132 | tosubmittotal=`echo "$totalpno - $queued" | bc -l`
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| 133 | fi
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| 134 | ;;
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| 135 | *) echo "Please give an algorithm to calculate the number of allowed jobs."
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| 136 | exit
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| 137 | ;;
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| 138 | esac
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| 139 | echo `date +%F\ %T`" Total number of jobs to be submitted: "$tosubmittotal >> $jmscriptlog 2>&1
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| 140 |
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| 141 | # first loop to determine
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| 142 | # a) how many jobs of this script have to be done
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| 143 | # b) how many jobs of this script are running or queued
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| 144 | todo=()
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| 145 | tododb=()
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| 146 | for (( i=0 ; i < ${#scripts[@]} ; i++ ))
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| 147 | do
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| 148 | # set the step to be evaluated
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| 149 | step=${scriptscolname[$i]}
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| 150 | getstepinfo
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| 151 |
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| 152 | # check if the script is restricted to one node
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| 153 | # (i.e. where output of previous step(s) is stored)
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| 154 | # this information is taken from the steps.rc file
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| 155 | # currently this is implemented for sge only
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| 156 | # then get number of jobs to be done
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| 157 | if [ "$noderestricted" = "yes" ]
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| 158 | then
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| 159 | # get number of next node
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| 160 | if [ $numevaluated -ge $numrestrictedscripts ]
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| 161 | then
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| 162 | currentnode=`echo " $currentnode + 1 " | bc -l`
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| 163 | numevaluated=1
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| 164 | else
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| 165 | numevaluated=`echo " $numevaluated + 1 " | bc -l`
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| 166 | fi
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| 167 | if [ $currentnode -gt $maxnode ]
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| 168 | then
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| 169 | currentnode=$minnode
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| 170 | fi
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| 171 | # check if node is excluded
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| 172 | for excludednode in ${excludednodes[@]}
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| 173 | do
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| 174 | if [ $currentnode -eq $excludednode ]
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| 175 | then
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| 176 | echo `date +%F\ %T`" Node compute-0-$currentnode is currently excluded." >> $jmscriptlog 2>&1
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| 177 | continue 2
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| 178 | fi
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| 179 | done
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| 180 | # define requirement for submission
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| 181 | # FIXME: currently only for sge at isdc
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| 182 | echo `date +%F\ %T`" Checking for node $currentnode. " >> $jmscriptlog 2>&1
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| 183 | noderequirementsub=" -hard -l hostname=compute-0-${currentnode}"
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| 184 | noderequirementstat=" -l hostname=compute-0-${currentnode}"
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| 185 | # get number of jobs to be done from the DB
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| 186 | getstatus $currentnode >> $jmscriptlog 2>&1
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| 187 | else
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| 188 | noderequirementsub=""
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| 189 | noderequirementstat=""
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| 190 | # get number of jobs to be done from the DB
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| 191 | getstatus >> $jmscriptlog 2>&1
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| 192 | fi
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| 193 | # store the number of processes to be done for this script
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| 194 | todo[$i]=$numproc
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| 195 | tododb[$i]=$numproc
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| 196 |
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| 197 | # FIXME: sge cuts scriptname to 8 digits in qstat
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| 198 | # number of idle jobs, i.e. jobs waiting in the queue to run
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| 199 | # condor: 1
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| 200 | # sge: q
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| 201 | # pbs: Q
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| 202 | #q4=( `echo ${q[@]} | egrep -o \("${scripts[$i]}"Jobstatus1\|"${scripts[$i]}"Jobstatusq\|"${scripts[$i]}"JobstatusQ\)` )
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| 203 | q4=( `echo ${q[@]} | egrep -o \("$step"Jobstatus1\|"$step"Jobstatusq\|"$step"JobstatusQ\)` )
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| 204 | idlescript[$i]=${#q4[@]}
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| 205 |
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| 206 | #q2=( `echo ${q[@]} | egrep -o "${scripts[$i]}"`)
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| 207 | q2=( `echo ${q[@]} | egrep -o "$step"`)
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| 208 | queuedscript[$i]=${#q2[@]}
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| 209 |
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| 210 | stillfree[$i]=`echo "${maxjobs[$i]} - ${queuedscript[$i]} " | bc -l`
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| 211 |
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| 212 | if [ $numproc -eq 0 ] || [ ${todo[$i]} -le ${idlescript[$i]} ] || [ ${maxjobs[$i]} -le ${queuedscript[$i]} ]
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| 213 | then
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| 214 | # store the fraction of cpus to add it to another process
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| 215 | idleratio=`echo " ${ratio[$i]} + $idleratio " | bc -l`
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| 216 | ratio[$i]=0
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| 217 | todo[$i]=0
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| 218 | idlenum=$i
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| 219 | continue
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| 220 | fi
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| 221 | done
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| 222 | echo `date +%F\ %T`" Evaluated scripts: "${scripts[@]} >> $jmscriptlog 2>&1
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| 223 | echo `date +%F\ %T`" Running scripts: "${queuedscript[@]}" (max: "${maxjobs[@]}")" >> $jmscriptlog 2>&1
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| 224 | echo `date +%F\ %T`" Number of jobs to be done (from DB): "${tododb[@]} >> $jmscriptlog 2>&1
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| 225 | echo `date +%F\ %T`" Number of jobs to be done (updated): "${todo[@]} >> $jmscriptlog 2>&1
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| 226 | echo `date +%F\ %T`" Ratio: "${ratio[@]}" (idle: "$idleratio")" >> $jmscriptlog 2>&1
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| 227 |
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| 228 | # loop to update the ratio taking into account the ratio of
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| 229 | # a) steps where nothing has to done
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| 230 | # b) steps where already enough jobs are in the queue
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| 231 | # sum up this idle ratio
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| 232 | # determine for which step still most jobs have to be done
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| 233 | if ! [ "$idleratio" = "0" ]
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| 234 | then
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| 235 | addtoscript=
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| 236 | for (( i=0 ; i < ${#scripts[@]} ; i++ ))
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| 237 | do
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| 238 | if [ ${todo[$i]} -gt ${todo[$idlenum]} ] && [ ${todo[$i]} -gt 0 ]
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| 239 | then
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| 240 | if ! [ "$addtoscript" = "" ]
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| 241 | then
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| 242 | if [ ${todo[$i]} -lt ${todo[$addtoscript]} ]
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| 243 | then
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| 244 | continue
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| 245 | fi
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| 246 | fi
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| 247 | addtoscript=$i
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| 248 | fi
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| 249 | done
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| 250 |
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| 251 | # continue in case nothing has to be done for all steps
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| 252 | # else: update the ratio for the step where most jobs have to be done
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| 253 | # by adding the idle ratio
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| 254 | if [ "$addtoscript" = "" ]
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| 255 | then
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| 256 | echo `date +%F\ %T`" No jobs to be done for any step." >> $jmscriptlog 2>&1
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| 257 | sleepawhile "ok"
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| 258 | else
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| 259 | ratio[$addtoscript]=`echo " ${ratio[$addtoscript]} + $idleratio " | bc -l`
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| 260 | fi
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| 261 | fi
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| 262 | echo `date +%F\ %T`" Updated ratio: "${ratio[@]} >> $jmscriptlog 2>&1
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| 263 |
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| 264 |
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| 265 | # loop to submit jobs to queueing system
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| 266 | for (( i=0 ; i < ${#scripts[@]} ; i++ ))
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| 267 | do
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| 268 | # calculate number of jobs to be submitted
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| 269 | tosubmit=`echo "scale=0; $tosubmittotal * ${ratio[$i]} / 1 " | bc -l`
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| 270 | if [ ${todo[$i]} -lt $tosubmit ]
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| 271 | then
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| 272 | echo `date +%F\ %T`" Updating tosubmit for "${scripts[$i]}" from "$tosubmit" to "${todo[$i]} >> $jmscriptlog 2>&1
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| 273 | tosubmit=${todo[$i]}
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| 274 | fi
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| 275 | if [ $tosubmit -eq 0 ]
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| 276 | then
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| 277 | echo `date +%F\ %T`" No jobs to be submitted for script '"${scripts[$i]}"'" >> $jmscriptlog 2>&1
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| 278 | continue
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| 279 | fi
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| 280 | if [ $tosubmit -gt ${stillfree[$i]} ]
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| 281 | then
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| 282 | echo `date +%F\ %T`" Updating tosubmit for "${scripts[$i]}" from "$tosubmit" to "${stillfree[$i]} >> $jmscriptlog 2>&1
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| 283 | tosubmit=${stillfree[$i]}
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| 284 | fi
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| 285 |
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| 286 | # set the step to be evaluated
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| 287 | step=${scriptscolname[$i]}
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| 288 | # check if walltime has to be set
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| 289 | if [ "$setwalltime" = "yes" ]
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| 290 | then
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| 291 | walltime=${walltimes[$i]}
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| 292 | fi
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| 293 | # check if memory has to be set
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| 294 | if [ "$setpmem" = "yes" ]
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| 295 | then
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| 296 | pmem=${pmems[$i]}
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| 297 | fi
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| 298 |
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| 299 | # submit $tosubmit scripts to queuing system
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| 300 | #tosubmit=1 #workaround for test on fact cluster
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| 301 | echo `date +%F\ %T`" Submitting "$tosubmit" jobs for script '"${scripts[$i]}"' to "$queuesys >> $jmscriptlog 2>&1
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| 302 | date=`date +%Y-%m-%d`
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| 303 | if ! queuesubmit 2>> $jmerrorlog
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| 304 | then
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| 305 | echo `date`" WARN submitting job ($queuesys) failed" >> $jmerrorlog
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| 306 | echo `date +%F\ %T`" WARN $queuesys is not working -> sleeping $errorsleeptime [\$errorsleeptime]" >> $jmscriptlog 2>&1
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| 307 | printprocesslog "WARN submitting ${scripts[$i]} ($queuesys) failed"
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| 308 | sleepawhile "error"
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| 309 | fi
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| 310 | done
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| 311 | sleepawhile "ok"
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| 312 | done
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| 313 |
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