| 1 | #!/bin/bash
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| 2 |
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| 3 | # this script has been written to run on La Palma on the machine newdata
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| 4 | # i.e. paths are only working on this machine
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| 5 |
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| 6 | # to use script with /data1 instead of /scratch
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| 7 | # (e.g. when /scratch is full)
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| 8 | # export data1=yes
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| 9 | # before executing the script
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| 10 | source `dirname $0`/../Sourcefile.sh
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| 11 | printprocesslog "INFO starting "$0
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| 12 |
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| 13 | logfile=$runlogpath"/ZipRawLP-"$datetime".log"
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| 14 | date >> $logfile
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| 15 |
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| 16 | if ! ls /scratch/raw >/dev/null 2>&1
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| 17 | then
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| 18 | printprocesslog "ERROR /scratch/raw is not available."
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| 19 | finish
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| 20 | fi
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| 21 |
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| 22 | # get dates
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| 23 | if [ "$certaindate" != "" ]
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| 24 | then
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| 25 | getdates $certaindate
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| 26 | else
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| 27 | # get all night
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| 28 | #getdates "all"
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| 29 | # get last 3 nights if hour between 7 and 19h, else only current night
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| 30 | getdates 3 7 19
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| 31 | fi
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| 32 |
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| 33 | rsynctempdir=/data1/rsync_tmp
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| 34 | if ! [ -d $rsynctempdir ]
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| 35 | then
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| 36 | mkdir $rsynctempdir
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| 37 | fi
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| 38 |
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| 39 | # not needed anymore as ftools are not used anymore
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| 40 | ## setup to use ftools
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| 41 | #source $HEADAS/headas-init.sh
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| 42 |
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| 43 | # files younger than $delaytime minutes are not processed
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| 44 | delaytime=5
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| 45 |
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| 46 | # do rsync for rawfiles of these dates
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| 47 | for date in ${dates[@]}
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| 48 | do
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| 49 | echo "" >> $logfile 2>&1
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| 50 | if [ "$data1" = "yes" ]
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| 51 | then
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| 52 | rawdir=/data1/raw/$date
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| 53 | printprocesslog "INFO using "$rawdir" as input"
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| 54 | else
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| 55 | rawdir=/scratch/raw/$date
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| 56 | fi
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| 57 | echo `date`": processing files in "$rawdir >> $logfile 2>&1
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| 58 | printprocesslog "INFO processing files in "$rawdir
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| 59 | #echo "INFO processing files in "$rawdir
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| 60 | # check if data are available from that night
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| 61 | if ! [ -d $rawdir ]
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| 62 | then
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| 63 | echo `date`": no data available in "$rawdir >> $logfile 2>&1
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| 64 | printprocesslog "INFO no data available in "$rawdir
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| 65 | continue
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| 66 | fi
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| 67 |
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| 68 | # find all fits-files starting with the oldest file
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| 69 | echo `date`": finding files to be zipped in $rawdir..." >> $logfile 2>&1
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| 70 | printprocesslog "INFO finding files to be zipped in "$rawdir"..."
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| 71 | fitsfiles=`find $rawdir -type f -regex '.*[.]fits[.]?[g]?[f]?[z]?' | sort `
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| 72 |
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| 73 | if [ ${#fitsfiles[@]} -eq 0 ]
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| 74 | then
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| 75 | echo `date`": no files to be zipped in $rawdir..." >> $logfile 2>&1
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| 76 | printprocesslog "INFO no files to be zipped in "$rawdir"..."
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| 77 | continue
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| 78 | fi
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| 79 |
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| 80 | rawdir2=/data1/raw/$date
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| 81 | zipdir=/data2/zipraw/$date
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| 82 | # create output directories
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| 83 | makedir $rawdir2 >> $logfile 2>&1
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| 84 | makedir $zipdir >> $logfile 2>&1
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| 85 |
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| 86 | # loop to zip files
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| 87 | echo `date`": zipping files in $rawdir..." >> $logfile 2>&1
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| 88 | printprocesslog "INFO zipping files in "$rawdir"..."
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| 89 | for file in $fitsfiles
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| 90 | do
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| 91 | # check if more than ~ 10 GB are left on output directories
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| 92 | diskusage=( `df -P /data1 | grep /data1 ` )
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| 93 | if [ ${diskusage[3]} -lt 10000000 ]
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| 94 | then
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| 95 | echo "WARN less than 10 GB left on /data1 on newdata ("${diskusage[3]}")" >> $logfile 2>&1
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| 96 | printprocesslog "WARN less than 10 GB left on /data1 on newdata ("${diskusage[3]}")"
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| 97 | finish
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| 98 | fi
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| 99 | diskusage=( `df -P /data2 | grep /data2 ` )
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| 100 | if [ ${diskusage[3]} -lt 10000000 ]
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| 101 | then
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| 102 | echo "WARN less than 10 GB left on /data2 on newdata ("${diskusage[3]}")" >> $logfile 2>&1
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| 103 | printprocesslog "WARN less than 10 GB left on /data2 on newdata ("${diskusage[3]}")"
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| 104 | finish
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| 105 | fi
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| 106 |
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| 107 | # check if raw file was accessed in the last $delaytime minutes
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| 108 | isnew=`find $file -amin -$delaytime`
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| 109 | if [ "$isnew" != "" ]
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| 110 | then
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| 111 | echo $file" is not older than $delaytime min => continue" >> $logfile 2>&1
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| 112 | printprocesslog "INFO "$file" is not older than $delaytime min => continue"
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| 113 | continue
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| 114 | fi
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| 115 |
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| 116 | printprocesslog "INFO process file "$file
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| 117 | if [ "$certaindate" != "" ]
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| 118 | then
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| 119 | echo "INFO process file "$file
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| 120 | fi
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| 121 | # first rsync from /scratch to /data1
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| 122 | if [ "$data1" != "yes" ]
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| 123 | then
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| 124 | file2=`echo $file | sed -e 's/scratch/data1/'`
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| 125 | if ! rsync -au -T $rsynctempdir $file $file2
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| 126 | then
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| 127 | printprocesslog "ERROR something went wrong with rsync of "$file
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| 128 | rm $file2
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| 129 | continue
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| 130 | fi
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| 131 | fi
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| 132 | # copying to /data2
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| 133 | iszipped=`echo $file | grep -o fz`
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| 134 | if [ "$iszipped" == "fz" ]
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| 135 | then
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| 136 | # treat already compressed files
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| 137 | printprocesslog "DEBUG treat compressed file "$file
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| 138 |
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| 139 | # filename for file on data
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| 140 | if [ "$data1" = "yes" ]
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| 141 | then
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| 142 | zipfile=`echo $file | sed -e 's/data1/data2/g' -e 's/raw/zipraw/' `
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| 143 | zipfiletmp=`echo $file | sed -e 's/data1/data2/g' -e 's/raw/zipraw/' -e 's/fits.fz/fits.fz.tmp/'`
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| 144 | else
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| 145 | zipfile=`echo $file | sed -e 's/scratch/data2/g' -e 's/raw/zipraw/' `
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| 146 | zipfiletmp=`echo $file | sed -e 's/scratch/data2/g' -e 's/raw/zipraw/' -e 's/fits.fz/fits.fz.tmp/'`
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| 147 | fi
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| 148 | # check if file on data already exists
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| 149 | if [ -e $zipfile ]
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| 150 | then
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| 151 | continue
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| 152 | fi
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| 153 |
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| 154 | echo `date`": copying "$file" to "$zipfile" ..." >> $logfile 2>&1
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| 155 | printprocesslog "INFO copying "$file" to "$zipfile" ..."
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| 156 | #echo "INFO zipping "$file" to "$zipfile" ..."
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| 157 | # read setup again to allow for updates of variables defining transfer
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| 158 | source `dirname $0`/../Sourcefile.sh
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| 159 | # zip file to stdout and pipe it to outputfile
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| 160 | echo "pv --rate-limit $limitpigz $file > $zipfiletmp" >> $logfile 2>&1
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| 161 | pv --rate-limit $limitpigz $file > $zipfiletmp
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| 162 | statuspv=$?
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| 163 | printprocesslog "DEBUG pvstatus:"$statuspv
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| 164 | echo " pvstatus:"$statuspv >> $logfile 2>&1
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| 165 | if [ $statuspv -eq 0 ]
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| 166 | then
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| 167 | # if successful, move temporary to final zipfile
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| 168 | printprocesslog "INFO move "$zipfiletmp" to "$zipfile" ..."
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| 169 | mv -v $zipfiletmp $zipfile >> $logfile 2>&1
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| 170 | else
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| 171 | # if not successful, remove temporary zipfile
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| 172 | printprocesslog "WARN pv failed (statuspv:"$statuspv")."
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| 173 | echo "WARN pv failed (PIPESTATUS:"$statuspv")." >> $logfile 2>&1
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| 174 | printprocesslog "INFO remove "$zipfiletmp"..."
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| 175 | rm -v $zipfiletmp >> $logfile 2>&1
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| 176 | finish
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| 177 | fi
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| 178 | else
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| 179 | # treat uncompressed files
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| 180 | printprocesslog "DEBUG treat uncompressed file "$file
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| 181 |
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| 182 | # filename for temporary and final zipfile
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| 183 | if [ "$data1" = "yes" ]
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| 184 | then
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| 185 | zipfile=`echo $file | sed -e 's/data1/data2/g' -e 's/raw/zipraw/' -e 's/fits/fits.gz/'`
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| 186 | zipfiletmp=`echo $file | sed -e 's/data1/data2/g' -e 's/raw/zipraw/' -e 's/fits/fits.tmp.gz/'`
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| 187 | else
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| 188 | zipfile=`echo $file | sed -e 's/scratch/data2/g' -e 's/raw/zipraw/' -e 's/fits/fits.gz/'`
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| 189 | zipfiletmp=`echo $file | sed -e 's/scratch/data2/g' -e 's/raw/zipraw/' -e 's/fits/fits.tmp.gz/'`
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| 190 | fi
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| 191 |
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| 192 | # check if zipped file already exists
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| 193 | if [ -e $zipfile ]
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| 194 | then
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| 195 | continue
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| 196 | fi
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| 197 |
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| 198 | echo `date`": zipping "$file" to "$zipfile" ..." >> $logfile 2>&1
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| 199 | printprocesslog "INFO zipping "$file" to "$zipfile" ..."
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| 200 | #echo "INFO zipping "$file" to "$zipfile" ..."
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| 201 | # read setup again to allow for updates of variables defining transfer
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| 202 | source `dirname $0`/../Sourcefile.sh
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| 203 | # zip file to stdout and pipe it to outputfile
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| 204 | echo "pv --rate-limit $limitpigz $file | pigz -1 -c -f -p $numprocpigz > $zipfiletmp" >> $logfile 2>&1
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| 205 | pv --rate-limit $limitpigz $file | pigz -1 -c -f -p $numprocpigz > $zipfiletmp
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| 206 | statuspigz=( `echo ${PIPESTATUS[@]}` )
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| 207 | printprocesslog "DEBUG PIPESTATUS:"${statuspigz[@]}
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| 208 | echo " PIPESTATUS:"${statuspigz[@]} >> $logfile 2>&1
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| 209 | if [ ${statuspigz[0]} -eq 0 ] && [ ${statuspigz[1]} -eq 0 ]
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| 210 | then
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| 211 | # if successful, move temporary to final zipfile
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| 212 | printprocesslog "INFO move "$zipfiletmp" to "$zipfile" ..."
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| 213 | mv -v $zipfiletmp $zipfile >> $logfile 2>&1
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| 214 | else
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| 215 | # if not successful, remove temporary zipfile
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| 216 | printprocesslog "WARN pigz or pv failed (PIPESTATUS:"${statuspigz[@]}")."
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| 217 | echo "WARN pigz or pv failed (PIPESTATUS:"${statuspigz[@]}")." >> $logfile 2>&1
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| 218 | printprocesslog "INFO remove "$zipfiletmp"..."
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| 219 | rm -v $zipfiletmp >> $logfile 2>&1
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| 220 | finish
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| 221 | fi
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| 222 | fi
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| 223 | done
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| 224 | done
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| 225 | echo "finished zipping..." >> $logfile 2>&1
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| 226 | finish
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