| [535] | 1 | #!/bin/sh -xvf
|
|---|
| 2 | #Perform the ON-OFF analysis
|
|---|
| 3 | DATE=/bin/date
|
|---|
| 4 | GREP=/bin/grep
|
|---|
| 5 | AWK=/bin/awk
|
|---|
| 6 | ECHO=/bin/echo
|
|---|
| 7 | WC=/usr/bin/wc
|
|---|
| 8 | CAT=/bin/cat
|
|---|
| 9 | PRINTF=/usr/bin/printf
|
|---|
| 10 | FIND=/usr/bin/find
|
|---|
| 11 | MKDIR=/bin/mkdir
|
|---|
| 12 | XARGS=/usr/bin/xargs
|
|---|
| 13 | SORT=/bin/sort
|
|---|
| 14 | RM=/bin/rm
|
|---|
| 15 | TR=/usr/bin/tr
|
|---|
| 16 | CP=/bin/cp
|
|---|
| 17 | LS=/bin/ls
|
|---|
| 18 | CHMOD=/bin/chmod
|
|---|
| 19 |
|
|---|
| 20 | DefaultIFS=$' \t\n'
|
|---|
| 21 | IFS=$DefaultIFS
|
|---|
| 22 |
|
|---|
| 23 | #set Irods environment
|
|---|
| 24 | . /usr/local/shared/bin/irods_env.sh -noverbose
|
|---|
| 25 |
|
|---|
| 26 | scriptName="`basename $0`"
|
|---|
| 27 | $ECHO "Processing script ${scriptName} at `date`"
|
|---|
| 28 | #which source to analyse
|
|---|
| 29 |
|
|---|
| 30 | #Process cmd line args: the -src option is mandatory (source name as Abell85)
|
|---|
| 31 | sourceRadio=
|
|---|
| 32 | dateSelected=
|
|---|
| 33 | #use -sim option to simulate processing (debug the script as if...)
|
|---|
| 34 | simulationMode=Off
|
|---|
| 35 | while [ $# -gt 0 ]
|
|---|
| 36 | do
|
|---|
| 37 | case "$1" in
|
|---|
| 38 | -src) sourceRadio=$2; shift;;
|
|---|
| [540] | 39 | -date) dateSelected=$2; shift;;
|
|---|
| 40 | -sim) simulationMode=On;;
|
|---|
| 41 | -h)
|
|---|
| 42 | echo >&2 \
|
|---|
| 43 | "usage: $0 -src souce -date YYYYMMDD [-freq freq in MHz (default ${freqBAOCalib})] [-sim to trig simulation mode]"
|
|---|
| 44 | exit 1;;
|
|---|
| 45 | *) break;; # terminate while loop
|
|---|
| 46 | esac
|
|---|
| 47 | shift
|
|---|
| [535] | 48 | done
|
|---|
| 49 |
|
|---|
| 50 | if [ ${simulationMode} = "On" ]; then
|
|---|
| 51 | $ECHO "INFO ${scriptName} running in SIMUL mode"
|
|---|
| 52 | fi
|
|---|
| 53 |
|
|---|
| 54 | if [ "<${sourceRadio}>" = "<>" ]; then
|
|---|
| 55 | $ECHO "FATAL: You have forgotten to select the source option (-src)"
|
|---|
| 56 | exit 1
|
|---|
| 57 | fi
|
|---|
| 58 |
|
|---|
| 59 | case ${sourceRadio} in
|
|---|
| 60 | Abell85) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
|
|---|
| 61 | Abell2440) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
|
|---|
| 62 | Abell1205) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
|
|---|
| 63 | *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen"
|
|---|
| 64 | exit 1;;
|
|---|
| 65 | esac
|
|---|
| 66 |
|
|---|
| 67 | srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" `
|
|---|
| 68 |
|
|---|
| 69 | #Path to public backupable path
|
|---|
| 70 | publicpath="/afs/in2p3.fr/home/c/campagne/public"
|
|---|
| 71 |
|
|---|
| 72 |
|
|---|
| 73 | #temporary files to synchronize scripts
|
|---|
| 74 | tmppublicpath=${TMPPUBLICPATH}
|
|---|
| 75 | #wakeup the NFS disk
|
|---|
| 76 | $LS -l ${tmppublicpath} > /dev/null
|
|---|
| 77 | #clean previous spurious files
|
|---|
| 78 | $RM -f ${tmppublicpath}/*.finished
|
|---|
| 79 |
|
|---|
| 80 | #Path where the job will do temporary IO
|
|---|
| 81 | if [ ${ENVIRONMENT} = "INTERACTIVE" ]; then
|
|---|
| 82 | iojobpath="/sps/baoradio/AmasNancay/JEC"
|
|---|
| 83 | $MKDIR -p $iojobpath
|
|---|
| [542] | 84 | $ECHO "Usage in INTERACTIVE may be destructive... To be used with great care !!!!"
|
|---|
| 85 | exit 0;
|
|---|
| [535] | 86 | elif [ ${ENVIRONMENT} = "BATCH" ] ; then
|
|---|
| 87 | iojobpath=${TMPBATCH}
|
|---|
| 88 | else
|
|---|
| 89 | $ECHO "FATAL (${scriptName}): environment is ${ENVIRONMENT} not allowed"
|
|---|
| 90 | exit 1
|
|---|
| 91 | fi
|
|---|
| 92 | cd ${iojobpath}
|
|---|
| 93 |
|
|---|
| 94 | localpath="${sourceRadio}"
|
|---|
| 95 | $MKDIR -p ./${localpath}
|
|---|
| 96 | cd ./${localpath}
|
|---|
| 97 |
|
|---|
| 98 | #save the top directory
|
|---|
| 99 | topDir=`pwd`
|
|---|
| 100 |
|
|---|
| 101 | #Path of the utility scripts
|
|---|
| 102 | scriptpath="/afs/in2p3.fr/home/c/campagne/private/work/AmasNancay"
|
|---|
| 103 |
|
|---|
| [540] | 104 | #JEC 1/10/11 Use generic baodaqstatus name
|
|---|
| [535] | 105 | #get the daq current irod status
|
|---|
| [540] | 106 | #tag=`${DATE} +%F`
|
|---|
| 107 | #OUT1=${publicpath}/baodaqstatus-${tag}.txt
|
|---|
| 108 | OUT1=${publicpath}/baodaqstatus-current.txt
|
|---|
| [535] | 109 |
|
|---|
| 110 | if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then
|
|---|
| [540] | 111 | $ECHO "FATAL (${scriptName}): ${OUT1} has a problem"
|
|---|
| 112 | exit 1
|
|---|
| 113 | # $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..."
|
|---|
| 114 | # $RM -f ${tmppublicpath}/statusdaq.finished
|
|---|
| 115 | # ${scriptpath}/statusdaq.sh > ${OUT1}
|
|---|
| 116 | # while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do
|
|---|
| 117 | # sleep 30
|
|---|
| 118 | # done
|
|---|
| 119 | # $RM ${tmppublicpath}/statusdaq.finished
|
|---|
| [535] | 120 | #protect against remove/rewriting
|
|---|
| [540] | 121 | # $CHMOD -v 444 ${OUT1}
|
|---|
| [535] | 122 | fi
|
|---|
| 123 |
|
|---|
| 124 |
|
|---|
| 125 |
|
|---|
| 126 | $ECHO "You have selected sourceRadio = ${sourceRadio} [date = ${dateSelected}]"
|
|---|
| 127 | tableau=( `$GREP -i "${dateSelected}${srclower}" ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` )
|
|---|
| 128 | IFS='
|
|---|
| 129 | '
|
|---|
| 130 | tableau=( $( $PRINTF "%s\n" "${tableau[@]}" | $AWK 'x[$0]++ == 0' ) )
|
|---|
| 131 | IFS=$DefaultIFS
|
|---|
| 132 |
|
|---|
| 133 |
|
|---|
| 134 | for i in ${tableau[@]}
|
|---|
| 135 | do
|
|---|
| 136 | #
|
|---|
| 137 | # start a "fresh" session
|
|---|
| 138 | cd ${topDir}
|
|---|
| 139 | $LS | $XARGS -i $RM -rf {}
|
|---|
| 140 |
|
|---|
| 141 | $ECHO "DEBUG: (${scriptName}) irods root dir $i"
|
|---|
| 142 | dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"`
|
|---|
| 143 |
|
|---|
| 144 | $ECHO "DEBUG: (${scriptName}): we are in directory `pwd` the topDir=${topDir}"
|
|---|
| 145 | $LS -lrt
|
|---|
| 146 |
|
|---|
| 147 |
|
|---|
| [540] | 148 | #JEC 1/10/11 Use generic baodaqstatus name
|
|---|
| [535] | 149 | #Look if the date has changed since beginning of the job!
|
|---|
| [540] | 150 | # curtag=`${DATE} +%F`
|
|---|
| 151 | # if [ "<${curtag}>" != "<${tag}>" ]; then
|
|---|
| 152 | # tag=${curtag}
|
|---|
| [535] | 153 | #it is necessary to update the daq status as the day has changed during the processing... (batch can take a long time...)
|
|---|
| [540] | 154 | # OUT1=${publicpath}/baodaqstatus-${curtag}.txt
|
|---|
| 155 | # $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..."
|
|---|
| 156 | # $RM -f ${tmppublicpath}/statusdaq.finished
|
|---|
| 157 | # ${scriptpath}/statusdaq.sh > ${OUT1}
|
|---|
| 158 | # while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do
|
|---|
| 159 | # sleep 30
|
|---|
| 160 | # done
|
|---|
| 161 | # $RM ${tmppublicpath}/statusdaq.finished
|
|---|
| [535] | 162 | #protect against remove/rewriting
|
|---|
| [540] | 163 | # $CHMOD -v 444 ${OUT1}
|
|---|
| 164 | # fi
|
|---|
| [535] | 165 | #
|
|---|
| 166 | # look if the gain & calibration files exist
|
|---|
| 167 | #
|
|---|
| 168 | gainDone=`ils ${i} 2>&1 | $GREP -i "gain_.*\.fits" | $WC -l`
|
|---|
| 169 | if [ ! ${gainDone} -gt 0 ]; then
|
|---|
| 170 | $ECHO "FATAL (${scriptName}): gain file DOES NOT exist skip `basename $i` "
|
|---|
| 171 | continue
|
|---|
| 172 | fi
|
|---|
| 173 |
|
|---|
| 174 | ######
|
|---|
| 175 | $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}"
|
|---|
| 176 | #go to the .../source/date-sourcelowercase directory
|
|---|
| 177 | #download Off/datacycle<> and On/datacycle<> directories
|
|---|
| 178 | $MKDIR -p ${topDir}/${dateDAQ}${srclower}
|
|---|
| 179 | cd ${topDir}/${dateDAQ}${srclower}
|
|---|
| 180 | aboveOnOffDir=`pwd`
|
|---|
| 181 | $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>"
|
|---|
| 182 | #
|
|---|
| 183 | mode="Off"
|
|---|
| 184 | $ECHO "DEBUG (${scriptName}): START download the ${mode} data fits files"
|
|---|
| 185 | inFileDirectory="./${mode}"
|
|---|
| 186 | $MKDIR -p ${inFileDirectory}
|
|---|
| 187 | listOfDataCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "datacycle"|$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.10n` )
|
|---|
| 188 | IFS='
|
|---|
| 189 | '
|
|---|
| 190 | listOfDataCycle=( $( $PRINTF "%s\n" "${listOfDataCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
|
|---|
| 191 | IFS=$DefaultIFS
|
|---|
| 192 |
|
|---|
| 193 | firstCycleOff=`$ECHO ${listOfDataCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
|
|---|
| 194 | nCyclesOff=`expr ${#listOfDataCycle[*]} - 1`
|
|---|
| 195 |
|
|---|
| 196 | if [ ${nCyclesOff} -eq -1 ]; then
|
|---|
| 197 | continue
|
|---|
| 198 | fi
|
|---|
| 199 |
|
|---|
| 200 | lastCycleOff=`$ECHO ${listOfDataCycle[${nCyclesOff}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
|
|---|
| 201 |
|
|---|
| 202 | listOfDataCycle=( "${listOfDataCycle[@]/#/${i}/${mode}/}" )
|
|---|
| 203 |
|
|---|
| 204 |
|
|---|
| 205 | for j in ${listOfDataCycle[@]}
|
|---|
| 206 | do
|
|---|
| 207 | irodsDownDir="${j}"
|
|---|
| 208 | OUT=./getInFits.$$
|
|---|
| 209 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
|
|---|
| 210 | igetStatus=`$GREP "^ERROR" ${OUT}`
|
|---|
| 211 | if [ "<$igetStatus>" != "<>" ]; then
|
|---|
| 212 | $ECHO "FATAL (${scriptName}): error while iget fits files:"
|
|---|
| 213 | $ECHO $igetStatus
|
|---|
| 214 | $ECHO " ==> skip this run $sourceRadio $dateDAQ"
|
|---|
| 215 | continue
|
|---|
| 216 | fi
|
|---|
| 217 | $RM -f ${OUT}
|
|---|
| 218 | done
|
|---|
| 219 | $ECHO "DEBUG (${scriptName}): END download the ${mode} data fits files"
|
|---|
| 220 | #
|
|---|
| 221 | mode="On"
|
|---|
| 222 | $ECHO "DEBUG (${scriptName}): START download the ${mode} data fits files"
|
|---|
| 223 | inFileDirectory="./${mode}"
|
|---|
| 224 | $MKDIR -p ${inFileDirectory}
|
|---|
| 225 |
|
|---|
| 226 | listOfDataCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "datacycle" |$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.10n` )
|
|---|
| 227 | IFS='
|
|---|
| 228 | '
|
|---|
| 229 | listOfDataCycle=( $( $PRINTF "%s\n" "${listOfDataCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
|
|---|
| 230 | IFS=$DefaultIFS
|
|---|
| 231 |
|
|---|
| 232 | firstCycleOn=`$ECHO ${listOfDataCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
|
|---|
| 233 | nCyclesOn=`expr ${#listOfDataCycle[*]} - 1`
|
|---|
| 234 |
|
|---|
| 235 | if [ ${nCyclesOn} -eq -1 ]; then
|
|---|
| 236 | continue
|
|---|
| 237 | fi
|
|---|
| 238 |
|
|---|
| 239 | lastCycleOn=`$ECHO ${listOfDataCycle[${nCyclesOn}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
|
|---|
| 240 |
|
|---|
| 241 | listOfDataCycle=( "${listOfDataCycle[@]/#/${i}/${mode}/}" )
|
|---|
| 242 |
|
|---|
| 243 | #
|
|---|
| 244 | #Check if there is the same number of cycles in Off and On mode
|
|---|
| 245 | #
|
|---|
| 246 | #first cycle = max(firstCycleOn, firstCycleOff)
|
|---|
| 247 | #last cycle = min(lastCycleOn,lastCycleOff)
|
|---|
| 248 |
|
|---|
| 249 | if [ ${firstCycleOn} -eq ${firstCycleOff} -a ${lastCycleOn} -eq ${lastCycleOff} ]; then
|
|---|
| 250 | firstCycle=${firstCycleOff}
|
|---|
| 251 | lastCycle=${lastCycleOff}
|
|---|
| 252 | else
|
|---|
| 253 | $ECHO "INFO (${scriptName}): missmatch between Off and On mode"
|
|---|
| 254 | $ECHO "${firstCycleOn} != ${firstCycleOff} OR ${lastCycleOn} != ${lastCycleOff}"
|
|---|
| 255 | firstCycle=${firstCycleOff}
|
|---|
| 256 | if [ ${firstCycleOn} -gt ${firstCycle} ]; then
|
|---|
| 257 | firstCycle=${firstCycleOn}
|
|---|
| 258 | fi
|
|---|
| 259 | lastCycle=${lastCycleOff}
|
|---|
| 260 | if [ ${lastCycleOn} -lt ${lastCycle} ]; then
|
|---|
| 261 | lastCycle=${lastCycleOn}
|
|---|
| 262 | fi
|
|---|
| 263 | fi
|
|---|
| 264 | $ECHO "INFO (${scriptName}): use cycles [${firstCycle}, ${lastCycle}]"
|
|---|
| 265 |
|
|---|
| 266 |
|
|---|
| 267 | for j in ${listOfDataCycle[@]}
|
|---|
| 268 | do
|
|---|
| 269 | irodsDownDir="${j}"
|
|---|
| 270 | OUT=./getInFits.$$
|
|---|
| 271 | iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
|
|---|
| 272 | igetStatus=`$GREP "^ERROR" ${OUT}`
|
|---|
| 273 | if [ "<$igetStatus>" != "<>" ]; then
|
|---|
| 274 | $ECHO "FATAL (${scriptName}): error while iget fits files:"
|
|---|
| 275 | $ECHO $igetStatus
|
|---|
| 276 | $ECHO " ==> skip this run $sourceRadio $dateDAQ"
|
|---|
| 277 | continue
|
|---|
| 278 | fi
|
|---|
| 279 | $RM -f ${OUT}
|
|---|
| 280 | done
|
|---|
| 281 | $ECHO "DEBUG (${scriptName}): END download the ${mode} data fits files"
|
|---|
| 282 | #Get sca file
|
|---|
| 283 | $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}"
|
|---|
| 284 | OUT1=./getScaStatus.$$
|
|---|
| 285 | $RM -f ${tmppublicpath}/getscafiles.finished
|
|---|
| 286 | ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1
|
|---|
| 287 | while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do
|
|---|
| 288 | $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished"
|
|---|
| 289 | date +%T
|
|---|
| 290 | sleep 30
|
|---|
| 291 | done
|
|---|
| 292 | $RM ${tmppublicpath}/getscafiles.finished
|
|---|
| 293 | $ECHO "DEBUG (${scriptName}): END"
|
|---|
| 294 | #
|
|---|
| 295 | getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}`
|
|---|
| 296 | #
|
|---|
| 297 | if [ "<${getScaStatus}>" != "<>" ]; then
|
|---|
| 298 | $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ"
|
|---|
| 299 | $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
|
|---|
| 300 | $CAT ${OUT1}
|
|---|
| 301 | $ECHO "DEBUG (${scriptName}): END"
|
|---|
| 302 | continue
|
|---|
| 303 | fi
|
|---|
| 304 | $RM -f ${OUT1}
|
|---|
| 305 |
|
|---|
| 306 | scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}`
|
|---|
| 307 |
|
|---|
| 308 |
|
|---|
| 309 | #prepare job submission
|
|---|
| 310 | cd ${aboveOnOffDir}
|
|---|
| 311 | #the default spectra name is medfiltmtx, otherwise use -specname <a_string>
|
|---|
| 312 |
|
|---|
| 313 | logFile="analyse_RAWDATA_${sourceRadio}_${dateDAQ}.log"
|
|---|
| 314 | $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`"
|
|---|
| 315 | if [ ${simulationMode} = "On" ]; then
|
|---|
| 316 | $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act rawOnOff -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir datacycle -numcycle ${firstCycle},${lastCycle} -debug 1 >& ${logFile}"
|
|---|
| 317 | cat > ${logFile} <<EOF
|
|---|
| 318 | Ok rawOnOff finished
|
|---|
| 319 | EOF
|
|---|
| 320 | else
|
|---|
| 321 | ${scriptpath}/Objs/analyse -act rawOnOff -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir datacycle -numcycle ${firstCycle},${lastCycle} -debug 1 >& ${logFile}
|
|---|
| 322 | fi
|
|---|
| 323 | $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods"
|
|---|
| 324 | rcstatus=`$GREP -i "Ok rawOnOff finished" ${logFile} | $WC -l`
|
|---|
| 325 | if [ ${rcstatus} -eq 0 ]; then
|
|---|
| 326 | $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}"
|
|---|
| 327 | $ECHO " START logfile"
|
|---|
| 328 | $CAT ${logFile}
|
|---|
| 329 | $ECHO " END logFile"
|
|---|
| 330 | #clean and leave
|
|---|
| 331 | cd ${aboveOnOffDir}
|
|---|
| 332 | $LS | $XARGS -i $RM -rf {}
|
|---|
| 333 | continue
|
|---|
| 334 | fi
|
|---|
| 335 | #Save into Irods
|
|---|
| 336 | $ECHO "DEBUG (${scriptName}): START save output files"
|
|---|
| 337 | $LS ${aboveOnOffDir}
|
|---|
| 338 | #use -f option for iput ONLY to force override
|
|---|
| 339 | if [ ${simulationMode} = "On" ]; then
|
|---|
| 340 | $ECHO "SIMUL: here we look for output files and put them in Irods"
|
|---|
| 341 | else
|
|---|
| 342 | $LS -lrth
|
|---|
| 343 | $FIND . -name "dataRaw_*" -print | $XARGS -i iput -f -v -K {} ${i}
|
|---|
| 344 | $FIND . -name "diffOnOffRaw_*" -print | $XARGS -i iput -f -v -K {} ${i}
|
|---|
| 345 | fi
|
|---|
| 346 | #save analysis logfile
|
|---|
| 347 | $LS -l ${tmppublicpath} > /dev/null
|
|---|
| 348 | $CP ${logFile} ${tmppublicpath}
|
|---|
| 349 | $ECHO "DEBUG (${scriptName}): END save output files"
|
|---|
| 350 | #clean up to avoid scratch SIZE EXCEED LIMIT
|
|---|
| 351 | cd ${aboveOnOffDir}
|
|---|
| 352 | $LS | $XARGS -i $RM -rf {}
|
|---|
| 353 |
|
|---|
| 354 | done
|
|---|
| 355 |
|
|---|
| 356 | exit 0
|
|---|
