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