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 |
---|