source: BAORadio/AmasNancay/v5/calibmaker.sh@ 634

Last change on this file since 634 was 579, checked in by torrento, 14 years ago

version adaptee a grid engin (ana)

File size: 14.5 KB
Line 
1#!/bin/sh -xvf
2#download SCA file, proceed to introspection, and upload results
3DATE=/bin/date
4GREP=/bin/grep
5AWK=/bin/awk
6ECHO=/bin/echo
7WC=/usr/bin/wc
8CAT=/bin/cat
9PRINTF=/usr/bin/printf
10FIND=/usr/bin/find
11MKDIR=/bin/mkdir
12XARGS=/usr/bin/xargs
13SORT=/bin/sort
14RM=/bin/rm
15TR=/usr/bin/tr
16CP=/bin/cp
17LS=/bin/ls
18CHMOD=/bin/chmod
19
20DefaultIFS=$' \t\n'
21IFS=$DefaultIFS
22
23#set Irods environment
24. /usr/local/shared/bin/irods_env.sh -noverbose
25
26scriptName="`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)
31sourceRadio=
32freqBAOCalib=1346
33bwBAOCalib=6.25
34#use -sim option to simulate processing (debug the script as if...)
35simulationMode=Off
36while [ $# -gt 0 ]
37do
38 case "$1" in
39 -src) sourceRadio=$2; shift;;
40 -freq) freqBAOCalib=$2; shift;;
41 -bwd) bwBAOCalib=$2; shift;;
42 -sim) simulationMode=On;;
43 -h)
44 echo >&2 \
45 "usage: $0 -src souce [-freq freq in MHz (default ${freqBAOCalib})] [-bwd bandwidth in MHz (default ${bwBAOCalib})]"
46 exit 1;;
47 *) break;; # terminate while loop
48 esac
49 shift
50done
51
52if [ ${simulationMode} = "On" ]; then
53 $ECHO "INFO ${scriptName} running in SIMUL mode"
54fi
55
56if [ "<${sourceRadio}>" = "<>" ]; then
57 $ECHO "FATAL: You have forgotten to select the source option (-src)"
58 exit 1
59fi
60
61case ${sourceRadio} in
62 Abell85) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
63 Abell2440) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
64 Abell1205) $ECHO "INFO (${scriptName}): process ${sourceRadio}";;
65 *) ECHO "FATAL (${scriptName}): process ${sourceRadio} not yet foreseen"
66 exit 1;;
67esac
68
69srclower=`${ECHO} ${sourceRadio} | ${TR} "[:upper:]" "[:lower:]" `
70
71#Path to public backupable path
72publicpath="/afs/in2p3.fr/home/c/campagne/public"
73
74
75#temporary files to synchronize scripts
76tmppublicpath=${TMPPUBLICPATH}
77#wakeup the NFS disk
78$LS -l ${tmppublicpath} > /dev/null
79#clean previous spurious files
80$RM -f ${tmppublicpath}/*.finished
81
82#Path where the job will do temporary IO
83. ${SCRIPTPATH}/isInteractive.sh
84isInteractive=$(isInteractive)
85if [ ${isInteractive} == "1" ]; then
86 $ECHO "Usage in INTERACTIVE may be destructive... To be used with great care !!!!"
87 exit 0;
88fi
89
90. ${SCRIPTPATH}/set_iojobpath.sh
91iojobpath=$(set_iojobpath)
92cd ${iojobpath}
93
94localpath="${sourceRadio}"
95$MKDIR -p ./${localpath}
96cd ./${localpath}
97
98#save the top directory
99topDir=`pwd`
100
101#Path of the utility scripts
102scriptpath=${SCRIPTPATH}
103
104#JEC 1/10/11 Use generic baodaqstatus name
105OUT1=${publicpath}/baodaqstatus-current.txt
106#
107#get the daq current irod status
108#tag=`${DATE} +%F`
109#OUT1=${publicpath}/baodaqstatus-${tag}.txt
110#
111if [ ! -e ${OUT1} -o ! -r ${OUT1} ]; then
112 $ECHO "FATAL (${scriptName}): ${OUT1} has a problem"
113 exit 1
114# $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..."
115# $RM -f ${tmppublicpath}/statusdaq.finished
116# ${scriptpath}/statusdaq.sh > ${OUT1}
117# while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do
118# sleep 30
119# done
120# $RM ${tmppublicpath}/statusdaq.finished
121#protect against remove/rewriting
122# $CHMOD -v 444 ${OUT1}
123fi
124
125
126#Nb: if we want to implement a loop on sources we have to take care of srclower...
127
128$ECHO "You have selected sourceRadio = $sourceRadio"
129tableau=( `$GREP -i ${sourceRadio} ${OUT1} | $AWK '( NF==4 ) { print $2 }' ` )
130IFS='
131'
132tableau=( $( $PRINTF "%s\n" "${tableau[@]}" | $AWK 'x[$0]++ == 0' ) )
133IFS=$DefaultIFS
134
135
136for i in ${tableau[@]}
137 do
138#
139# start a "fresh" session
140 cd ${topDir}
141 $LS | $XARGS -i $RM -rf {}
142
143
144 $ECHO "DEBUG: (${scriptName}) irods root dir $i"
145 dateDAQ=`$ECHO ${i} | $AWK '{split($0,a,"/"); print a[6];}' | $AWK "{sub(/${srclower}/,\"\"); print}"`
146
147 $ECHO "DEBUG: (${scriptName}): we are in directory `pwd` the topDir=${topDir}"
148 $LS -lrt
149
150
151#JEC 1/10/11 Use generic baodaqstatus name
152#Look if the date has changed since beginning of the job!
153# curtag=`${DATE} +%F`
154# if [ "<${curtag}>" != "<${tag}>" ]; then
155# tag=${curtag}
156#it is necessary to update the daq status as the day has changed during the processing... (batch can take a long time...)
157# OUT1=${publicpath}/baodaqstatus-${curtag}.txt
158# $ECHO "We should bring the DAQ status more up to date, this take 1 or 2sec..."
159# $RM -f ${tmppublicpath}/statusdaq.finished
160# ${scriptpath}/statusdaq.sh > ${OUT1}
161# while [ ! -f "${tmppublicpath}/statusdaq.finished" ]; do
162# sleep 30
163# done
164# $RM ${tmppublicpath}/statusdaq.finished
165#protect against remove/rewriting
166# $CHMOD -v 444 ${OUT1}
167# fi
168#
169# look if the calibration files already exist
170#
171 alreadyDone=`ils ${i} 2>&1 | $GREP -i "calib_.*\.txt" | $WC -l`
172 if [ ${alreadyDone} -gt 0 ]; then
173 $ECHO "INFO (${scriptName}): calibration coef files already exist"
174 continue
175 fi
176#
177 somethingTodo=1
178 input4calibOff=`ils ${i}/Off 2>&1 | $GREP -i "calibcycle" | $AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n`
179 input4calibOn=`ils ${i}/On 2>&1 | $GREP -i "calibcycle" | $AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n`
180#
181 if [ "<${input4calibOff}>" != "<>" -a "<${input4calibOn}>" != "<>" ]; then
182#look at the content of the calibcycle directory as may be the previous batch job has crashed
183 tableauOff=( `$ECHO ${input4calibOff}` )
184 IFS='
185'
186 tableauOff=( $( $PRINTF "%s\n" "${tableauOff[@]}" | $AWK 'x[$0]++ == 0' ) )
187 IFS=$DefaultIFS
188#
189 nTotFilesOff=0
190 for j in ${tableauOff[@]}
191 do
192 nFiles=`ils ${i}/Off/${j} | $GREP -i "medfiltmtx" | $WC -l`
193 nTotFilesOff=`expr ${nTotFilesOff} + ${nFiles}`
194 done
195#
196 tableauOn=( `$ECHO ${input4calibOn}` )
197 IFS='
198 '
199 tableauOn=( $( $PRINTF "%s\n" "${tableauOn[@]}" | $AWK 'x[$0]++ == 0' ) )
200 IFS=$DefaultIFS
201#
202 nTotFilesOn=0
203 for j in ${tableauOn[@]}
204 do
205 nFiles=`ils ${i}/On/${j} | $GREP -i "medfiltmtx" | $WC -l`
206 nTotFilesOn=`expr ${nTotFilesOn} + ${nFiles}`
207 done
208 diffOnOff=`expr ${nTotFilesOff} - ${nTotFilesOn}`
209 if [ ${diffOnOff} -lt 0 ]; then
210 zero=0
211 diffOnOff=`expr ${zero} - ${diffOnOff}`
212 fi
213#allow up to 5 files differences
214 if [ ${nTotFilesOff} -gt 0 -a ${nTotFilesOn} -gt 0 ]; then
215 somethingTodo=0
216 $ECHO "DEBUG (${scriptName}): $sourceRadio $dateDAQ has <${nTotFilesOff}> Off-files and <${nTotFilesOn}> On-files but OK"
217 else
218 $ECHO "INFO (${scriptName}): $sourceRadio $dateDAQ has <${nTotFilesOff}> Off-files and <${nTotFilesOn}> On-files => one should rebuild has something is wrong"
219 fi
220#
221 fi
222 if [ ${somethingTodo} -eq 1 ]; then
223#
224 $ECHO ">>>>>>>>>>>>>>>> Do $sourceRadio $dateDAQ CALIBOFF"
225 $RM -f ${tmppublicpath}/proc_script.finished
226 if [ ${simulationMode} = "On" ]; then
227 $ECHO "SIMUL: ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBOFF"
228 else
229 ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBOFF
230 while [ ! -e "${tmppublicpath}/proc_script.finished" ]; do
231 $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/proc_script.finished"
232 date +%T
233 sleep 60
234 done
235 fi
236 $ECHO "INFO (${scriptName}): proc_script has finished"
237 $ECHO ">>>>>>>>>>>> Done $sourceRadio $dateDAQ CALIBOFF"
238 $ECHO ">>>>>>>>>>>>>>>> Do $sourceRadio $dateDAQ CALIBON"
239 $RM ${tmppublicpath}/proc_script.finished
240
241 if [ ${simulationMode} = "On" ]; then
242 $ECHO "SIMUL: ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBON"
243 else
244 ${scriptpath}/proc_script.sh $sourceRadio $dateDAQ CALIBON
245 while [ ! -e "${tmppublicpath}/proc_script.finished" ]; do
246 $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/proc_script.finished"
247 date +%T
248 sleep 60
249 done
250 fi
251 $ECHO "INFO (${scriptName}): proc_script has finished"
252 $RM ${tmppublicpath}/proc_script.finished
253#Todo see if there is errors in the log file before copy
254 $ECHO ">>>>>>>>>>>> Done $sourceRadio $dateDAQ CALIBON"
255######
256 else
257######
258 $ECHO ">>>>>>>>>>>>> ANALYSIS Part of ${sourceRadio} ${dateDAQ}"
259 #go to the .../source/date-sourcelowercase directory
260#download Off/calibcycle<> and On/calibcycle<> directories
261 $MKDIR -p ${topDir}/${dateDAQ}${srclower}
262 cd ${topDir}/${dateDAQ}${srclower}
263 aboveOnOffDir=`pwd`
264 $ECHO "DEBUG (${scriptName}): we are in directory: <`pwd`>"
265#
266 mode="Off"
267 $ECHO "DEBUG (${scriptName}): START download the ${mode} calib fits files"
268 inFileDirectory="./${mode}"
269 $MKDIR -p ${inFileDirectory}
270 listOfCalibCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "calibcycle"|$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n` )
271 IFS='
272'
273 listOfCalibCycle=( $( $PRINTF "%s\n" "${listOfCalibCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
274 IFS=$DefaultIFS
275
276 firstCycleOff=`$ECHO ${listOfCalibCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
277 nCyclesOff=`expr ${#listOfCalibCycle[*]} - 1`
278
279 lastCycleOff=`$ECHO ${listOfCalibCycle[${nCyclesOff}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
280
281 listOfCalibCycle=( "${listOfCalibCycle[@]/#/${i}/${mode}/}" )
282
283
284 for j in ${listOfCalibCycle[@]}
285 do
286 irodsDownDir="${j}"
287 OUT=./getInFits.$$
288 iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
289 igetStatus=`$GREP "^ERROR" ${OUT}`
290 if [ "<$igetStatus>" != "<>" ]; then
291 $ECHO "FATAL (${scriptName}): error while iget fits files:"
292 $ECHO $igetStatus
293 $ECHO " ==> skip this run $sourceRadio $dateDAQ"
294 continue
295 fi
296 $RM -f ${OUT}
297 done
298 $ECHO "DEBUG (${scriptName}): END download the ${mode} calib fits files"
299#
300 mode="On"
301 $ECHO "DEBUG (${scriptName}): START download the ${mode} calib fits files"
302 inFileDirectory="./${mode}"
303 $MKDIR -p ${inFileDirectory}
304
305 listOfCalibCycle=( `ils ${i}/${mode} 2>&1 | $GREP -i "calibcycle" |$AWK 'BEGIN{FS="C- "}{print $2}' | $XARGS -i basename {} | $SORT -k1.11n` )
306 IFS='
307'
308 listOfCalibCycle=( $( $PRINTF "%s\n" "${listOfCalibCycle[@]}" | $AWK 'x[$0]++ == 0' ) )
309 IFS=$DefaultIFS
310
311 firstCycleOn=`$ECHO ${listOfCalibCycle[0]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
312 nCyclesOn=`expr ${#listOfCalibCycle[*]} - 1`
313
314 lastCycleOn=`$ECHO ${listOfCalibCycle[${nCyclesOn}]} | $AWK '{match($0,"[0-9]+",arr); print arr[0]}'`
315
316 listOfCalibCycle=( "${listOfCalibCycle[@]/#/${i}/${mode}/}" )
317
318
319#
320#Check if there is the same number of cycles in Off and On mode
321#
322#first cycle = max(firstCycleOn, firstCycleOff)
323#last cycle = min(lastCycleOn,lastCycleOff)
324
325 if [ ${firstCycleOn} -eq ${firstCycleOff} -a ${lastCycleOn} -eq ${lastCycleOff} ]; then
326 firstCycle=${firstCycleOff}
327 lastCycle=${lastCycleOff}
328 else
329 $ECHO "INFO (${scriptName}): missmatch between Off and On mode"
330 $ECHO "${firstCycleOn} != ${firstCycleOff} OR ${lastCycleOn} != ${lastCycleOff}"
331 firstCycle=${firstCycleOff}
332 if [ ${firstCycleOn} -gt ${firstCycle} ]; then
333 firstCycle=${firstCycleOn}
334 fi
335 lastCycle=${lastCycleOff}
336 if [ ${lastCycleOn} -lt ${lastCycle} ]; then
337 lastCycle=${lastCycleOn}
338 fi
339 fi
340 $ECHO "INFO (${scriptName}): use cycles [${firstCycle}, ${lastCycle}]"
341
342
343 for j in ${listOfCalibCycle[@]}
344 do
345 irodsDownDir="${j}"
346 OUT=./getInFits.$$
347 iget -r -f -K ${irodsDownDir} ${inFileDirectory} > ${OUT} 2>&1
348 igetStatus=`$GREP "^ERROR" ${OUT}`
349 if [ "<$igetStatus>" != "<>" ]; then
350 $ECHO "FATAL (${scriptName}): error while iget fits files:"
351 $ECHO $igetStatus
352 $ECHO " ==> skip this run $sourceRadio $dateDAQ"
353 continue
354 fi
355 $RM -f ${OUT}
356 done
357 $ECHO "DEBUG (${scriptName}): END download the ${mode} calib fits files"
358#Get sca file
359 $ECHO "DEBUG (${scriptName}): START call getscafiles.sh ${sourceRadio} ${dateDAQ}"
360 OUT1=./getScaStatus.$$
361 $RM -f ${tmppublicpath}/getscafiles.finished
362 ${scriptpath}/getscafiles.sh ${sourceRadio} ${dateDAQ} > ${OUT1} 2>&1
363 while [ ! -f "${tmppublicpath}/getscafiles.finished" ]; do
364 $ECHO "INFO (${scriptName}): waiting for ${tmppublicpath}/getscafiles.finished"
365 date +%T
366 sleep 30
367 done
368 $RM ${tmppublicpath}/getscafiles.finished
369 $ECHO "DEBUG (${scriptName}): END"
370#
371 getScaStatus=`$GREP "^\(FATAL\|ERROR\)" ${OUT1}`
372#
373 if [ "<${getScaStatus}>" != "<>" ]; then
374 $ECHO "FATAL (${scriptName}): error to get sca file for $sourceRadio $dateDAQ"
375 $ECHO "DEBUG (${scriptName}): START with cat ${OUT1}"
376 $CAT ${OUT1}
377 $ECHO "DEBUG (${scriptName}): END"
378 continue
379 fi
380 $RM -f ${OUT1}
381
382 scaFile=`$FIND . -name "sca*.sum.trans" | $XARGS -i basename {}`
383
384#prepare job submission
385 cd ${aboveOnOffDir}
386#the default spectra name is medfiltmtx, otherwise use -specname <a_string>
387
388 logFile="analyse_CALIB_${sourceRadio}_${dateDAQ}.log"
389 $ECHO "DEBUG (${scriptName}): execute the analysis... should not take long. `date`"
390 if [ ${simulationMode} = "On" ]; then
391 $ECHO "SIMUL: ${scriptpath}/Objs/analyse -act calib -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir calibcycle -numcycle ${firstCycle},${lastCycle} -calibopt mean -debuglev 1 -freqBAOCalib ${freqBAOCalib} -bwBAOCalib ${bwBAOCalib} >& ${logFile}"
392 cat > ${logFile} <<EOF
393 Ok calibration finished
394EOF
395 else
396 ${scriptpath}/Objs/analyse -act calib -inPath ${iojobpath} -source ${sourceRadio} -date ${dateDAQ} -sca ${scaFile} -specdir calibcycle -numcycle ${firstCycle},${lastCycle} -calibopt mean -debuglev 1 -freqBAOCalib ${freqBAOCalib} -bwBAOCalib ${bwBAOCalib} >& ${logFile}
397 fi
398 $ECHO "DEBUG (${scriptName}): analysis finished `date`. Look for errors before saving to Irods"
399 rcstatus=`$GREP -i "Ok calibration finished" ${logFile} | $WC -l`
400 if [ ${rcstatus} -eq 0 ]; then
401 $ECHO "INFO (${scriptName}): analysis problem for ${sourceRadio} ${dateDAQ}"
402 $ECHO " START logfile"
403 $CAT ${logFile}
404 $ECHO " END logFile"
405#clean and leave
406 cd ${aboveOnOffDir}
407 $LS | $XARGS -i $RM -rf {}
408 continue
409 fi
410#Save into Irods
411 $ECHO "DEBUG (${scriptName}): START save output files"
412 $LS ${aboveOnOffDir}
413#use -f option for iput ONLY to force override
414 if [ ${simulationMode} = "On" ]; then
415 $ECHO "SIMUL: here we look for calib file and put them in Irods"
416 else
417 $FIND . -name "calib_*" -print | $XARGS -i iput -v -K {} ${i}
418 fi
419#save analysis logfile
420 $LS -l ${tmppublicpath} > /dev/null
421 $CP ${logFile} ${tmppublicpath}
422 $ECHO "DEBUG (${scriptName}): END save output files"
423#clean up to avoid scratch SIZE EXCEED LIMIT
424 cd ${aboveOnOffDir}
425 $LS | $XARGS -i $RM -rf {}
426 fi
427done
428
429exit 0
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