| 1 | #!/bin/sh -xvf
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| 2 | #Basic tuning of system fuction used.
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| 3 | AWK=/bin/awk
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| 4 | SED=/bin/sed
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| 5 | GREP=/bin/grep
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| 6 | WC=/usr/bin/wc
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| 7 | RM=/bin/rm
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| 8 | CAT=/bin/cat
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| 9 | TOUCH=/bin/touch
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| 10 | DATE=/bin/date
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| 11 | ECHO=/bin/echo
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| 12 | LS=/bin/ls
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| 13 | MKDIR=/bin/mkdir
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| 14 | TR=/usr/bin/tr
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| 15 | FIND=/usr/bin/find
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| 16 | PRINTF=/usr/bin/printf
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| 17 | XARGS=/usr/bin/xargs
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| 18 | SORT=/bin/sort
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| 19 | QSUB=qsub
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| 20 |
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| 21 | DefaultIFS=$' \t\n'
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| 22 | IFS=$DefaultIFS
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| 23 |
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| 24 |
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| 25 | scriptName="`basename $0`"
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| 26 | $ECHO "Processing script ${scriptName} at `date`"
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| 27 | ######
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| 28 | # Local functions
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| 29 | ######
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| 30 | usage() {
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| 31 | echo "usage: $scriptName <source> <YYYYMMDD-directory> <type of process>"
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| 32 | echo " -<source> as Abell85"
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| 33 | echo " -<YYYYMMDD-directory> as 20110428"
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| 34 | echo " -<type of process> as GAIN|CALIBON|CALIBOFF|ON|OFF"
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| 35 | }
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| 36 | ######
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| 37 | # argument test
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| 38 | ######
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| 39 | if [ ! $# = 3 ]; then
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| 40 | usage
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| 41 | touch proc_script.finished
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| 42 | exit 1
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| 43 | fi
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| 44 | sourceRadio=$1
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| 45 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" `
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| 46 | dateDAQ=$2
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| 47 | typeofproc=$3
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| 48 |
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| 49 | #Path to public backupable path
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| 50 | publicpath="/afs/in2p3.fr/home/c/campagne/public"
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| 51 |
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| 52 | #temporary files to synchronize scripts
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| 53 | tmppublicpath=${TMPPUBLICPATH}
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| 54 | $LS -l ${tmppublicpath} > /dev/null
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| 55 |
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| 56 |
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| 57 | #Path where the job will do temporary IO
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| 58 | if [ ${ENVIRONMENT} = "INTERACTIVE" ]; then
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| 59 | iojobpath="/sps/baoradio/AmasNancay/JEC"
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| 60 | $MKDIR -p $iojobpath
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| 61 | elif [ ${ENVIRONMENT} = "BATCH" ] ; then
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| 62 | iojobpath=${TMPBATCH}
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| 63 | else
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| 64 | $ECHO "FATAL (${scriptName}): environment is ${ENVIRONMENT} not allowed"
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| 65 | touch ${tmppublicpath}/proc_script.finished
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| 66 | exit 1
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| 67 | fi
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| 68 | cd ${iojobpath}
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| 69 |
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| 70 | localpath="${sourceRadio}/${dateDAQ}${srclower}"
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| 71 | $MKDIR -p ./${localpath}
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| 72 | cd ./${localpath}
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| 73 | mainDirectory=`pwd`
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| 74 |
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| 75 |
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| 76 | #Path of the utility scripts
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| 77 | scriptpath=${SCRIPTPATH}
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| 78 |
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| 79 |
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| 80 | #select file per cycle
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| 81 | #$ECHO "Select files process..."
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| 82 | #keep only lines with structure: cycle_number first,last,step
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| 83 | #Get sca files
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| 84 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}"
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| 85 | OUT1=./getScaStatus.$$
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| 86 | $RM -f ${tmppublicpath}/getscafiles.finished
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| 87 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1
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| 88 | while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do
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| 89 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished"
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| 90 | date +%T
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| 91 | sleep 30
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| 92 | done
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| 93 | $RM ${tmppublicpath}/getscafiles.finished
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| 94 | $ECHO "DEBUG (${scriptName}): END"
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| 95 |
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| 96 |
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| 97 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}`
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| 98 |
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| 99 | if [ "<${getScaStatus}>" != "<>" ]; then
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| 100 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ"
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| 101 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
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| 102 | $CAT ${OUT1}
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| 103 | $ECHO "DEBUG (${scriptName}): END"
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| 104 | touch ${tmppublicpath}/proc_script.finished
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| 105 | exit 1
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| 106 | fi
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| 107 |
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| 108 |
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| 109 | scaFileSummarized=`$FIND . -name "sca*.sum" -print`
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| 110 | if [ "<${scaFileSummarized}>" = "<>" ]; then
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| 111 | $ECHO "FATAL (${scriptName}): strange sca file summarized not available: $sourceRadio $dateDAQ"
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| 112 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
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| 113 | $CAT ${OUT1}
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| 114 | $ECHO "DEBUG (${scriptName}): END"
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| 115 | touch ${tmppublicpath}/proc_script.finished
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| 116 | exit 1
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| 117 | fi
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| 118 | $RM ${OUT1}
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| 119 |
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| 120 | scaFileSummarized=`basename $scaFileSummarized`
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| 121 |
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| 122 | #set Irods environment
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| 123 | . /usr/local/shared/bin/irods_env.sh -noverbose
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| 124 | #download header files to be used for signal files selction
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| 125 | $MKDIR -p ./Fiber1
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| 126 | dirFiberfile=`pwd`/Fiber1
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| 127 |
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| 128 | dirIrods="/baoradio/data/AmasNancay/${sourceRadio}/${dateDAQ}${srclower}/Fiber1"
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| 129 |
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| 130 | listOfFiles=( `ils ${dirIrods} | $GREP -i "header" | $XARGS -i basename {} | $SORT -k1.7n` )
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| 131 | IFS='
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| 132 | '
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| 133 | listOfFiles=( $( $PRINTF "%s\n" "${listOfFiles[@]}" | $AWK 'x[$0]++ == 0' ) )
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| 134 | IFS=$DefaultIFS
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| 135 |
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| 136 | #
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| 137 | $ECHO "DEBUG (${scriptName}): Download if necessary the headers"
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| 138 | #
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| 139 | for ifile in ${listOfFiles[@]}
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| 140 | do
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| 141 | #test if the headers have not yet been downloaded
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| 142 | if [ ! -e ${dirFiberfile}/${ifile} ]; then
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| 143 | OUT2=./getheaders.$$
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| 144 | iget -f -K ${dirIrods}/${ifile} ${dirFiberfile} >${OUT2} 2>&1
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| 145 | igetStatus=`$GREP "^ERROR" ${OUT2}`
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| 146 | if [ "<$igetStatus>" != "<>" ]; then
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| 147 | $ECHO "FATAL (${scriptName}): error while iget:"
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| 148 | $ECHO $igetStatus
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| 149 | touch ${tmppublicpath}/proc_script.finished
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| 150 | exit 1
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| 151 | fi
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| 152 | $RM -f $OUT2
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| 153 | fi
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| 154 | done
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| 155 | #
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| 156 | $ECHO "DEBUG (${scriptName}): START call select.sh ${scaFileSummarized} ${dirFiberfile} ${typeofproc}"
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| 157 | #
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| 158 | #Get list of file to process
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| 159 | headerFileSelected=./selectSignal.$$
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| 160 | $RM -f ${tmppublicpath}/select.finished
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| 161 | ${scriptpath}/select.sh ${scaFileSummarized} ${dirFiberfile} ${typeofproc} | $GREP "^#[0-9]" | $SED "s/^#//" > $headerFileSelected
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| 162 | while [ ! -f "${tmppublicpath}/select.finished" ]; do
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| 163 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/select.finished"
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| 164 | date +%T
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| 165 | sleep 30
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| 166 | done
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| 167 | $RM ${tmppublicpath}/select.finished
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| 168 | #
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| 169 | $ECHO "DEBUG (${scriptName}): END"
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| 170 | #
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| 171 | $ECHO "DEBUG (${scriptName}): START filling cycleArray, filesArray"
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| 172 | #
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| 173 | declare -a cycleArray
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| 174 | declare -a filesArray
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| 175 | $ECHO "DEBUG (${scriptName}): IFS value between<>: <$IFS>"
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| 176 | IFS=$DefaultIFS
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| 177 | $ECHO "DEBUG (${scriptName}): START cat $headerFileSelected"
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| 178 | $CAT $headerFileSelected
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| 179 | $ECHO "DEBUG (${scriptName}): END cat $headerFileSelected"
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| 180 |
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| 181 | while read v1 v2
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| 182 | do
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| 183 | cycleArray[${#cycleArray[*]}]=$v1
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| 184 | filesArray[${#filesArray[*]}]=$v2
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| 185 | done < $headerFileSelected
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| 186 |
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| 187 | if [ ${#cycleArray[*]} -eq 0 -o ${#filesArray[*]} -eq 0 ]; then
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| 188 | $ECHO "FATAL (${scriptName}): no header file selected (${#cycleArray[*]}, ${#filesArray[*]})"
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| 189 | touch ${tmppublicpath}/proc_script.finished
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| 190 | exit 1
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| 191 | else
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| 192 | $ECHO "DEBUG (${scriptName}): non zero elements found for cycleArray and filesArray"
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| 193 | fi
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| 194 |
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| 195 | #
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| 196 | $ECHO "DEBUG (${scriptName}): number of elements <${#cycleArray[*]}> <${#filesArray[*]}>"
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| 197 | $ECHO "DEBUG (${scriptName}): END"
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| 198 | #
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| 199 | # (timeShift)
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| 200 | #Add 3sec to start ON / OFF
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| 201 | #Substract 4sec to start DAB ON / OFF
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| 202 | #
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| 203 | #Take care: Cycle numbering starts at 1 in SCAFiles while Arrays index start at 0
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| 204 | #
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| 205 | #for GAIN the reference cycle takes the middle of the run
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| 206 | #
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| 207 | #nwinmean donne le nombre de fenetre tspwin utilise pour faire calculer la moyenne des medianes de chaque fenetre
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| 208 | #This is the nimber of paquets of the time window which change according to processing type
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| 209 | $ECHO "DEBUG (${scriptName}): START switch on $typeofproc"
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| 210 | #
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| 211 | case "$typeofproc" in
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| 212 | GAIN)
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| 213 | $ECHO "process signal files for GAIN phase"
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| 214 | ingain=""
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| 215 | freqfilter="-freqfilter -"
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| 216 | nwinmean="1"
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| 217 | tspwin="5120"
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| 218 | dirName="Off"
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| 219 | cyclebasename="gaincycle"
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| 220 | indexStartHour="6"
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| 221 | timeShift="-4"
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| 222 | timeDuration="14"
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| 223 | firstCycleId=`expr ${#cycleArray[*]} / 2`
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| 224 | firstCycleId=`expr ${firstCycleId} - 1`
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| 225 | lastp1CycleId=`expr ${firstCycleId} + 1`
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| 226 | ;;
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| 227 | ON)
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| 228 | $ECHO "process signal files for ON phases"
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| 229 | ingain="-gain gain_${dateDAQ}_${srclower}.fits"
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| 230 | freqfilter="-freqfilter 16"
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| 231 | nwinmean="5"
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| 232 | tspwin="5120"
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| 233 | dirName="On"
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| 234 | cyclebasename="datacycle"
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| 235 | indexStartHour="4"
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| 236 | timeShift="3"
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| 237 | timeDuration="30"
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| 238 | firstCycleId="0"
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| 239 | lastp1CycleId="${#cycleArray[@]}"
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| 240 | ;;
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| 241 | OFF)
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| 242 | $ECHO "process signal files for OFF phases"
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| 243 | ingain="-gain gain_${dateDAQ}_${srclower}.fits"
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| 244 | freqfilter="-freqfilter 16"
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| 245 | nwinmean="5"
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| 246 | tspwin="5120"
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| 247 | dirName="Off"
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| 248 | cyclebasename="datacycle"
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| 249 | indexStartHour="8"
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| 250 | timeShift="3"
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| 251 | timeDuration="30"
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| 252 | firstCycleId="0"
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| 253 | lastp1CycleId="${#cycleArray[@]}"
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| 254 | ;;
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| 255 | CALIBON)
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| 256 | $ECHO "process signal files for CALIBRATION ON phases"
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| 257 | ingain="-gain gain_${dateDAQ}_${srclower}.fits"
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| 258 | freqfilter="-freqfilter 16"
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| 259 | nwinmean="1"
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| 260 | tspwin="1024"
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| 261 | dirName="On"
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| 262 | cyclebasename="calibcycle"
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| 263 | indexStartHour="2"
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| 264 | timeShift="-4"
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| 265 | timeDuration="14"
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| 266 | firstCycleId="0"
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| 267 | lastp1CycleId="${#cycleArray[@]}"
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| 268 | ;;
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| 269 | CALIBOFF)
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| 270 | $ECHO "process signal files for CALIBRATION OFF phases"
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| 271 | ingain="-gain gain_${dateDAQ}_${srclower}.fits"
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| 272 | freqfilter="-freqfilter 16"
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| 273 | nwinmean="1"
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| 274 | tspwin="1024"
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| 275 | dirName="Off"
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| 276 | cyclebasename="calibcycle"
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| 277 | indexStartHour="6"
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| 278 | timeShift="-4"
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| 279 | timeDuration="14"
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| 280 | firstCycleId="0"
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| 281 | lastp1CycleId="${#cycleArray[@]}"
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| 282 | ;;
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| 283 | *)
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| 284 | $ECHO "FATAL (${scriptName}): type of processing"
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| 285 | usage
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| 286 | touch ${tmppublicpath}/proc_script.finished
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| 287 | exit 1
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| 288 | ;;
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| 289 | esac
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| 290 | #
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| 291 | $ECHO "DEBUG (${scriptName}): END"
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| 292 | #
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| 293 | #
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| 294 | #Compute time windows (Warning usage of GMT date)
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| 295 | #
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| 296 | $ECHO "DEBUG (${scriptName}): START compute time windows"
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| 297 | OUT=./baotiming.$$
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| 298 | ${AWK} -v datesys=${DATE} -v type=${indexStartHour} -v shift=${timeShift} '
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| 299 | BEGIN {FS=","}
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| 300 | {
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| 301 | phaseStart=$type
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| 302 | cmd=sprintf("%s +%%s -d \"%s\" ",datesys,phaseStart);
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| 303 | (cmd | getline phstart);
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| 304 | close(cmd);
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| 305 | newstart = phstart+shift;
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| 306 | cmd=sprintf("%s +%%T -d \"1970-01-01 %s sec GMT\"",datesys,newstart);
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| 307 | (cmd | getline newStart);
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| 308 | close(cmd);
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| 309 | print $1,newStart,phaseStart;
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| 310 | }
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| 311 | ' ${scaFileSummarized} > ${OUT}
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| 312 | #
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| 313 | $ECHO "DEBUG (${scriptName}): END"
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| 314 | #
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| 315 | $ECHO "DEBUG (${scriptName}): START cat ${OUT}"
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| 316 | $CAT ${OUT}
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| 317 | $ECHO "DEBUG (${scriptName}): END cat ${OUT}"
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| 318 | #
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| 319 | $ECHO "DEBUG (${scriptName}): START filling cylceArrayBis timeArray"
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| 320 | #
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| 321 | declare -a cycleArrayBis
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| 322 | declare -a timeArray
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| 323 | $ECHO "DEBUG (${scriptName}): IFS value between<>: <$IFS>"
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| 324 | IFS=$DefaultIFS
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| 325 | #select the selected cycles
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| 326 | idtofind="0"
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| 327 | while read v1 v2 v3
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| 328 | do
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| 329 | if [ ${idtofind} -lt ${#cycleArray[*]} ]; then
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| 330 | if [ ${v1} = ${cycleArray[${idtofind}]} ]; then
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| 331 | cycleArrayBis[${#cycleArrayBis[*]}]=$v1
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| 332 | timeArray[${#timeArray[*]}]=$v2
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| 333 | idtofind=`expr ${idtofind} + 1`
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| 334 | fi
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| 335 | fi
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| 336 | done < ${OUT}
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| 337 | $ECHO "DEBUG (${scriptName}): number of elements ${#cycleArrayBis[*]} ${#timeArray[*]}"
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| 338 | $ECHO "DEBUG (${scriptName}): END"
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| 339 |
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| 340 |
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| 341 | #########################
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| 342 | # specmfib exe
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| 343 | #########################
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| 344 | prg="/afs/in2p3.fr/throng/baoradio/Library/Progs/TAcq/Objs/specmfib"
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| 345 | if [ ! -e $prg ]; then
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| 346 | $ECHO "FATAL (${scriptName}): $prg not found"
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| 347 | touch ${tmppublicpath}/proc_script.finished
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| 348 | exit 1
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| 349 | fi
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| 350 |
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| 351 |
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| 352 | dirFiberfile=${iojobpath}/${localpath}
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| 353 |
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| 354 | curDir=`pwd`
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| 355 | #
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| 356 | $ECHO "DEBUG (${scriptName}): in principle $dirFiberfile == $curDir "
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| 357 | #
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| 358 | #force single channel
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| 359 | forceSingle="-singlechan"
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| 360 | #debug
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| 361 | prtlevel="1"
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| 362 |
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| 363 |
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| 364 | #Loop on cycles to write batch script and send to batch queue
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| 365 | ##
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| 366 | $ECHO "DEBUG (${scriptName}): START loop on cycles ${firstCycleId} to ${lastp1CycleId}"
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| 367 |
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| 368 | for ((i=${firstCycleId};i<${lastp1CycleId};i++)); do
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| 369 | #
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| 370 | $ECHO "DEBUG (${scriptName}): process cycle $i"
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| 371 | #time window selection
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| 372 | tmproc="-tmproc ${timeArray[${i}]},${timeDuration}"
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| 373 | #cycle <name><number>
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| 374 | cycle="${cyclebasename}${cycleArray[${i}]}"
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| 375 | #signal files selection
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| 376 | infiles="${filesArray[${i}]}"
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| 377 | #
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| 378 | #Prepare BQS parameters: MEMORY, CPU...#
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| 379 | infilesArray=( `$ECHO $infiles | $AWK 'BEGIN {FS=","} {for(i=1;i<NF;i++)print $i;}'` )
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| 380 | IFS='
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| 381 | '
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| 382 | infilesArray=( $( printf "%s\n" "${infilesArray[@]}" | awk 'x[$0]++ == 0' ) )
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| 383 | IFS=$DefaultIFS
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| 384 | firstFile=${infilesArray[0]}
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| 385 | lastFile=${infilesArray[1]}
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| 386 | #compute Scratch Size MB (400MB per signal files), CPU Time
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| 387 | nFiles=`expr ${lastFile} - ${firstFile} + 1`
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| 388 | # Fiber 1 & Fiber 2 => double the number of files
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| 389 | nFiles=`expr ${nFiles} \* 2`
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| 390 | #add number of spectra generated (cf. (Nbrepaquets_per_files * nFiles /tspwin) * 100KB
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| 391 | nSpectra=`expr ${nFiles} \* 25600 / ${tspwin}`
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| 392 | #Guess formula to reserved the amount of space needed in scratch
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| 393 | scratchSize=`expr ${nFiles} \* 500 + ${nSpectra} \* 200 / 1000 + 5`
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| 394 | # 60sec/signal_file * empirical_conversion_factor (=50)
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| 395 | cpu=`expr ${nFiles} \* 60 \* 50`
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| 396 | #Virtual Memory (MB) Nb: at CCIN2P3 the reasonable max is 1GB
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| 397 | virtualmem=1000
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| 398 | #Job and batch names
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| 399 | jobBatchName="${sourceRadio}-${dateDAQ}-${typeofproc}-cycle${cycleArray[${i}]}"
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| 400 | jobScriptName="${jobBatchName}.sh"
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| 401 | jobLogName="${jobBatchName}.log"
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| 402 | #
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| 403 | $ECHO "DEBUG (${scriptName}): start writing ${jobScriptName}"
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| 404 | #
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| 405 | #
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| 406 | #write the script to be send to Batch
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| 407 | #
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| 408 | $CAT > ${jobScriptName} <<EOF
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| 409 | #!/bin/sh -xvf
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| 410 | # jobBatchName=$jobBatchName
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| 411 | # jobScriptName=$jobScriptName
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| 412 | # jobLogName=$jobLogName
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| 413 | scriptName=$jobScriptName
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| 414 |
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| 415 | . /afs/in2p3.fr/home/throng/baoradio/setup.sh
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| 416 | . /usr/local/shared/bin/irods_env.sh -noverbose
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| 417 |
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| 418 | iojobpath=\${TMPBATCH}
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| 419 | cd \${iojobpath}
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| 420 | localpath=${sourceRadio}/${dateDAQ}${srclower}
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| 421 | $MKDIR -p ./\${localpath}
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| 422 | cd ./\${localpath}
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| 423 |
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| 424 | curDir=\`pwd\`
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| 425 | #get gain file if necessary
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| 426 | if [ ${typeofproc} != "GAIN" ]; then
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| 427 | OUT2=./igetStatus.$$
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| 428 | iget /baoradio/data/AmasNancay/${localpath}/gain_${dateDAQ}_${srclower}.fits >\${OUT2} 2>&1
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| 429 | igetStatus=\`$GREP "^ERROR" \${OUT2}\`
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| 430 | if [ "<\${igetStatus}>" != "<>" ]; then
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| 431 | $ECHO "FATAL (\${scriptName}): error while iget:"
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| 432 | $ECHO \$igetStatus
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| 433 | touch ${tmppublicpath}/${jobBatchName}.finished
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| 434 | exit 1
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| 435 | fi
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| 436 | $RM \${OUT2}
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| 437 | fi
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| 438 | #get signals files
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| 439 | OUT3=./getsignals.$$
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| 440 | $RM -f ${tmppublicpath}/getsignalfiles.finished
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| 441 | ${scriptpath}/getsignalfiles.sh ${sourceRadio} ${dateDAQ} ${firstFile} ${lastFile} > \${OUT3} 2>&1
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| 442 | while [ ! -f "${tmppublicpath}/getsignalfiles.finished" ]; do
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| 443 | $ECHO "INFO (\${scriptName}): waiting for ${tmppublicpath}/getsignalfiles.finished"
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| 444 | date +%T
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| 445 | sleep 30
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| 446 | done
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| 447 | $RM ${tmppublicpath}/getsignalfiles.finished
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| 448 |
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| 449 | getSignals=\`$GREP "^FATAL" \${OUT3}\`
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|---|
| 450 | if [ "<\$getSignals>" != "<>" ]; then
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| 451 | $ECHO "FATAL (\${scriptName}): error while get signals"
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|---|
| 452 | $ECHO \$getSignals
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|---|
| 453 | touch ${tmppublicpath}/${jobBatchName}.finished
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| 454 | exit 1
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|---|
| 455 | fi
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| 456 | $RM \${OUT3}
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|---|
| 457 | #location of the signal file
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|---|
| 458 | fibfile="\${curDir} 1,2"
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| 459 | #
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| 460 | outDir=\${curDir}/${dirName}/${cycle}
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|---|
| 461 | $MKDIR -p \${outDir}
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|---|
| 462 |
|
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| 463 | #
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|---|
| 464 | # where ami...
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|---|
| 465 | #
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|---|
| 466 | $ECHO "We are here \`pwd\` to send the batch"
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|---|
| 467 | $LS -lrth
|
|---|
| 468 | $FIND . -name "igetStatus.*" | $XARGS -i $CAT {}
|
|---|
| 469 | $LS ./Fiber1 | $WC -l
|
|---|
| 470 | $LS ./Fiber2 | $WC -l
|
|---|
| 471 | $LS -lR \${outDir}
|
|---|
| 472 |
|
|---|
| 473 | #Note: here act=gain means only that specmfib will use median-like algorithms (not only for gains...)
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|---|
| 474 | $prg -act gain $forceSingle $freqfilter -prt $prtlevel -out \${outDir} -nmean $nwinmean $ingain $tmproc -tspwin ${tspwin},0,0 -in $infiles \${fibfile}
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| 475 |
|
|---|
| 476 | $ECHO \${outDir}
|
|---|
| 477 | $LS -lrt \${outDir}
|
|---|
| 478 |
|
|---|
| 479 | #save results to Irods (use option -f ONLY to force override)
|
|---|
| 480 | iput -v -K -r \${curDir}/${dirName} /baoradio/data/AmasNancay/\${localpath}
|
|---|
| 481 | #
|
|---|
| 482 | #clean the signal files which can at the end of the day fill completly the scratch directory of the batch work/AmasNancayer
|
|---|
| 483 | $RM -f \${iojobpath}/\${localpath}/Fiber1/signal*.fits
|
|---|
| 484 | $RM -f \${iojobpath}/\${localpath}/Fiber2/signal*.fits
|
|---|
| 485 | touch ${tmppublicpath}/${jobBatchName}.finished
|
|---|
| 486 | exit 0
|
|---|
| 487 | EOF
|
|---|
| 488 | #
|
|---|
| 489 | #The EOF tag MUST BEGIN the line, this is the end of the script
|
|---|
| 490 | #
|
|---|
| 491 | $ECHO "DEBUG (${scriptName}); START listing of script to be send to batch queue"
|
|---|
| 492 | $CAT -v ${jobScriptName}
|
|---|
| 493 | $ECHO "DEBUG (${scriptName}): END listing"
|
|---|
| 494 | #
|
|---|
| 495 | #send to BATCH
|
|---|
| 496 | #
|
|---|
| 497 | $ECHO "DEBUG (${scriptName}): START send to batch listing"
|
|---|
| 498 | #
|
|---|
| 499 | $RM -f ${tmppublicpath}/${jobBatchName}.finished
|
|---|
| 500 |
|
|---|
| 501 | ##26/9/11 JEC use option -h to trig manualy the job on the queue...
|
|---|
| 502 | qsub -h -l u_sps_baoradio,u_irods,u_irods_baoradio,T=${cpu},M=${virtualmem}MB,scratch=${scratchSize}MB,platform=LINUX -eo -o ${tmppublicpath}/${jobLogName} -N ${jobBatchName} ${jobScriptName}
|
|---|
| 503 |
|
|---|
| 504 | # while [ ! -f "${tmppublicpath}/${jobBatchName}.finished" ]; do
|
|---|
| 505 | # $ECHO "INFO (${scriptName}); waiting for ${tmppublicpath}/${jobBatchName}.finished"
|
|---|
| 506 | # date +%T
|
|---|
| 507 | # sleep 600
|
|---|
| 508 | # done
|
|---|
| 509 | # $RM ${tmppublicpath}/${jobBatchName}.finished
|
|---|
| 510 | $ECHO "DEBUG (${scriptName}): end send to batch listing"
|
|---|
| 511 | #end loop on cycles
|
|---|
| 512 | done
|
|---|
| 513 | #
|
|---|
| 514 | $ECHO "DEBUG (${scriptName}): END loop on cycles"
|
|---|
| 515 | #
|
|---|
| 516 | touch ${tmppublicpath}/proc_script.finished
|
|---|
| 517 | exit 0
|
|---|
