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handle bash args properly using arrays
[u/mrichter/AliRoot.git] / PWGPP / benchmark / benchmark.sh
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1#!/bin/bash
2#include benchmark.config
3
4# this script runs the CPass0/CPass1 train
5# produced OCDB updates are local
6
7main()
8{
9 #run in proper mode depending on the selection
10 if [[ $# -lt 1 ]]; then
11 if [[ ! "${0}" =~ "bash" ]]; then
12 echo "uses makeflow:"
13 echo " ${0} \"run\" productionID inputList configFile [extraOpts]"
14 echo "uses a batch system (SGE):"
15 echo " ${0} \"submit\" productionID inputList configFile [extraOpts]"
16 echo "extraOpts if non-empty override the config file, e.g.:"
17 echo " ${0} submit test1 benchmark.list benchmark.config runNumber=169123 nEvents=10"
18 fi
19 return
20 fi
21
22 #define some aliases - default is to call one of the functions directly
23 runMode=${1}
24 umask 0002
25 shift
26 case ${runMode} in
27 "CPass0") goCPass0 "$@";;
28 "CPass1") goCPass1 "$@";;
29 "MakeLocalOCDBaccessConfig") goMakeLocalOCDBaccessConfig "$@";;
30 "MergeCPass0") goMergeCPass0 "$@";;
31 "MergeCPass1") goMergeCPass1 "$@";;
32 "MakeFilteredTrees") goMakeFilteredTrees "$@";;
33 "MakeSummary") goMakeSummary "$@";;
34 "run") goSubmitMakeflow "$@";;
35 "submit") goSubmitBatch "$@";;
36 "test") goTest "$@";;
37 "GenerateMakeflow") goGenerateMakeflow "$@";;
38 "PrintValues") goPrintValues "$@";;
39 "CreateQAplots") goCreateQAplots "$@";;
40 "WaitForOutput") goWaitForOutput "$@";;
41 "Merge") goMerge "$@";;
42 *)
43 ${runMode} "$@"
44 ;;
45 esac
46}
47
48generateMC()
49{
50 #generate one raw chunk in current directory
51 SEED=${JOB_ID}${SGE_TASK_ID}
52 export CONFIG_SEED=${SEED}
53 runNumber=${1}
54 OCDBpath=${2}
55 nEventsim=${3}
56 if [[ -n ${pretend} ]]; then
57 touch galice.root
58 else
59 if [[ -f sim.C && -f Config.C ]] ; then
60 time aliroot -b -q -x sim.C\(${runNumber},\"${OCDBpath}\",${nEventsim}\) >sim.log 2>&1
61 mv syswatch.log simwatch.log
62 fi
63 fi
64}
65
66goCPass0()
67{
68 umask 0002
69
70 targetDirectory=${1}
71 inputList=${2}
72 nEvents=${3}
73 ocdbPath=${4}
74 configFile=${5}
75 runNumber=${6}
76 jobindex=${7}
77 shift 7
78 if ! parseConfig ${configFile} "$@"; then return 1; fi
79
80 #use the jobindex only if set and non-negative
81 if [[ -z ${jobindex} || ${jobindex} -lt 0 ]]; then
82 [[ -n "${LSB_JOBINDEX}" ]] && jobindex=${LSB_JOBINDEX}
83 [[ -n "${SGE_TASK_ID}" ]] && jobindex=${SGE_TASK_ID}
84 fi
85
86 [[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
87 doneFile="${commonOutputPath}/meta/cpass0.job${jobindex}.run${runNumber}.done"
88
89 [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
90
91 if [[ -n ${ALIROOT_FORCE_COREDUMP} ]]; then
92 ulimit -c unlimited
93 export ALIROOT_FORCE_COREDUMP
94 fi
95
96 #the contents of this is stored in the tree and used later (e.g. AliAnalysisTaskPIDResponse)!
97 #at the QA stage the pass number is guessed from the path stored here.
98 #The Format is:
99 #Packages= ;OutputDir= ;LPMPass= ;TriggerAlias= ;LPMRunNumber= ;LPMProductionType= ;LPMInteractionType= ;LPMProductionTag= ;LPMAnchorRun= ;LPMAnchorProduction= ;LPMAnchorYear=
100 export PRODUCTION_METADATA="OutputDir=cpass0"
101
102 if [[ "${inputList}" =~ \.root$ ]]; then
103 infile=${inputList}
104 else
105 infile=$(sed -ne "${jobindex}p" ${inputList} | egrep '\s*\w*/\w*')
106 fi
107 chunkName=${infile##*/}
108
109 outputDir=${targetDirectory}/${jobindex}_${chunkName%.*}
110 mkdir -p ${outputDir}
111 [[ ! -d ${outputDir} ]] && echo "cannot make ${outputDir}" && touch ${doneFile} && return 1
112
113 #runpath=${PWD}/rundir_cpass0_${runNumber}_${jobindex}
114 runpath=${outputDir}
115 [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
116 [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
117 mkdir -p ${runpath}
118 [[ ! -d ${runpath} ]] && echo "cannot make runpath ${runpath}" && touch ${doneFile} && return 1
119 cd ${runpath}
120
121 #runCPassX/C expects the raw chunk to be linked in the run dir
122 #despite it being accessed by the full path
123 ln -s ${infile} ${runpath}/${chunkName}
124
125 #####MC
126 if [[ -n ${generateMC} ]]; then
127 olddir=${PWD}
128 outputDirMC=${commonOutputPath}/000${runNumber}/sim/${jobindex}
129 simrunpath=${outputDirMC}
130 [[ ${simulateInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && simrunpath=${TMPDIR}
131 [[ ${simulateInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && simrunpath=$(mktemp -d)
132 mkdir -p ${outputDirMC}
133 mkdir -p ${simrunpath}
134 cd ${simrunpath}
135
136 filesMC=(
137 "${commonOutputPath}/sim.C"
138 "${commonOutputPath}/rec.C"
139 "${commonOutputPath}/Config.C"
140 "${commonOutputPath}/OCDB_*.root"
141 )
142 for file in ${filesMC[*]}; do
143 [[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
144 done
145
146 generateMC ${runNumber} ${ocdbPath} ${nEvents}
147
148 [[ ! "${simrunpath}" =~ "${outputDirMC}" ]] && mv * ${outputDirMC} #TODO check if it works
149 cd ${olddir}
150
151 ln -s ${outputDirMC}/* ${runpath}/
152
153 inputList=${outputDirMC}/galice.root #TODO not valid outside shell !!!
154 infile=""
155 fi
156 ######
157
158 [[ ! -f ${inputList} && -z ${pretend} ]] && echo "input file ${inputList} not found, exiting..." && touch ${doneFile} && return 1
159
160 logOutputDir=${runpath}
161 [[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
162 [[ -z ${dontRedirectStdOutToLog} ]] && exec 1> ${logOutputDir}/stdout
163 [[ -z ${dontRedirectStdOutToLog} ]] && exec 2> ${logOutputDir}/stderr
164 echo "${0} $*"
165
166 echo "#####################"
167 echo CPass0:
168 echo JOB setup
169 echo nEvents ${nEvents}
170 echo runNumber ${runNumber}
171 echo ocdbPath ${ocdbPath}
172 echo infile ${infile}
173 echo chunkName ${chunkName}
174 echo jobindex ${jobindex}
175 echo recoTriggerOptions ${recoTriggerOptions}
176 echo targetDirectory ${targetDirectory}
177 echo commonOutputPath ${commonOutputPath}
178 echo doneFile ${doneFile}
179 echo runpath ${runpath}
180 echo outputDir ${outputDir}
181 echo ALICE_ROOT ${ALICE_ROOT}
182 echo PWD ${PWD}
183 echo "########## ###########"
184
185 alirootInfo > ALICE_ROOT.log
186
187 filesCPass0=(
188 "${commonOutputPath}/runCPass0.sh"
189 "${commonOutputPath}/recCPass0.C"
190 "${commonOutputPath}/runCalibTrain.C"
191 "${commonOutputPath}/localOCDBaccessConfig.C"
192 "${commonOutputPath}/OCDB.root"
193 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/runCPass0.sh"
194 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/recCPass0.C"
195 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/runCalibTrain.C"
196 )
197
198 for file in ${filesCPass0[*]}; do
199 [[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
200 done
201
202 echo "this directory (${PWD}) contents:"
203 /bin/ls
204 echo
205 chmod u+x runCPass0.sh
206
207 sed -i '/.*root .*\.C/ s|\s*,\s*|,|g' *.sh
208
209 if [[ -n ${postSetUpActionCPass0} ]]; then
210 echo "running ${postSetUpActionCPass0}"
211 eval ${postSetUpActionCPass0}
212 fi
213
214 #run CPass0
215 echo "${runpath}/runCPass0.sh ${infile} ${nEvents} ${runNumber} ${ocdbPath} ${recoTriggerOptions}"
216 if [[ -n ${pretend} ]]; then
217 touch AliESDs.root
218 touch AliESDfriends.root
219 touch AliESDfriends_v1.root
220 touch rec.log
221 touch calib.log
222 else
223 echo ./runCPass0.sh "${infile}" "${nEvents}" "${runNumber}" "${ocdbPath}" "${recoTriggerOptions}"
224 ./runCPass0.sh "${infile}" "${nEvents}" "${runNumber}" "${ocdbPath}" "${recoTriggerOptions}"
225 fi
226
227 #move stuff to final destination
228 echo "this directory (${PWD}) contents:"
229 /bin/ls
230 echo
231
232 echo rm -f ./${chunkName}
233 rm -f ./${chunkName}
234 echo "cp --recursive ${runpath}/* ${outputDir}"
235 cp -p --recursive ${runpath}/* ${outputDir}
236 echo
237
238 #validate CPass0
239 cd ${outputDir}
240 touch ${doneFile}
241 echo "dir ${outputDir}" >> ${doneFile}
242 if summarizeLogs >> ${doneFile}; then
243 [[ -f ${outputDirMC}/galice.root ]] && echo "sim ${outputDirMC}/galice.root" >> ${doneFile}
244 [[ -f AliESDfriends_v1.root ]] && echo "calibfile ${outputDir}/AliESDfriends_v1.root" >> ${doneFile}
245 [[ -f AliESDs.root ]] && echo "esd ${outputDir}/AliESDs.root" >> ${doneFile}
246 fi
247
248 [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
249 return 0
250}
251
252goCPass1()
253{
254 umask 0002
255
256 targetDirectory=${1}
257 inputList=${2}
258 nEvents=${3}
259 ocdbPath=${4}
260 configFile=${5}
261 runNumber=${6}
262 jobindex=${7}
263 shift 7
264 extraOpts=("$@")
265 if ! parseConfig ${configFile} "$@"; then return 1; fi
266
267 #use the jobindex only if set and non-negative
268 if [[ -z ${jobindex} || ${jobindex} -lt 0 ]]; then
269 [[ -n "${LSB_JOBINDEX}" ]] && jobindex=${LSB_JOBINDEX}
270 [[ -n "${SGE_TASK_ID}" ]] && jobindex=${SGE_TASK_ID}
271 fi
272
273 [[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
274 doneFile="${commonOutputPath}/meta/cpass1.job${jobindex}.run${runNumber}.done"
275
276 [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
277
278 if [[ -n ${ALIROOT_FORCE_COREDUMP} ]]; then
279 ulimit -c unlimited
280 export ALIROOT_FORCE_COREDUMP
281 fi
282
283 #the contents of this is stored in the tree and used later (e.g. AliAnalysisTaskPIDResponse)!
284 #at the QA stage the pass number is guessed from the path stored here.
285 #The Format is:
286 #Packages= ;OutputDir= ;LPMPass= ;TriggerAlias= ;LPMRunNumber= ;LPMProductionType= ;LPMInteractionType= ;LPMProductionTag= ;LPMAnchorRun= ;LPMAnchorProduction= ;LPMAnchorYear=
287 export PRODUCTION_METADATA="OutputDir=cpass1"
288
289 [[ ! -f ${inputList} && -z ${pretend} ]] && echo "input file ${inputList} not found, exiting..." && touch ${doneFile} && return 1
290 if [[ "${inputList}" =~ \.root$ ]]; then
291 infile=${inputList}
292 else
293 infile=$(sed -ne "${jobindex}p" ${inputList} | egrep '\s*\w*/\w*')
294 fi
295 chunkName=${infile##*/}
296
297 outputDir=${targetDirectory}/${jobindex}_${chunkName%.*}
298 mkdir -p ${outputDir}
299 [[ ! -d ${outputDir} ]] && echo "cannot make ${outputDir}" && touch ${doneFile} && return 1
300
301 #runpath=${PWD}/rundir_cpass1_${runNumber}_${jobindex}
302 runpath=${outputDir}
303 [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
304 [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
305
306 #MC
307 if [[ "${infile}" =~ galice\.root ]]; then
308 ln -s ${inputList%/*}/* ${runpath}
309 infile=""
310 fi
311
312 #init the running path
313 mkdir -p ${runpath}
314 [[ ! -d ${runpath} ]] && echo "cannot make runpath ${runpath}" && touch ${doneFile} && return 1
315 cd ${runpath}
316
317 #this is needed for runCPass1.sh
318 ln -s ${infile} ${runpath}/${chunkName}
319
320 logOutputDir=${runpath}
321 [[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
322 [[ -z ${dontRedirectStdOutToLog} ]] && exec 1> ${logOutputDir}/stdout
323 [[ -z ${dontRedirectStdOutToLog} ]] && exec 2> ${logOutputDir}/stderr
324 echo "${0} $*"
325
326 echo "#####################"
327 echo CPass1:
328 echo JOB setup
329 echo nEvents ${nEvents}
330 echo runNumber ${runNumber}
331 echo ocdbPath ${ocdbPath}
332 echo infile ${infile}
333 echo chunkName ${chunkName}
334 echo jobindex ${jobindex}
335 echo recoTriggerOptions ${recoTriggerOptions}
336 echo targetDirectory ${targetDirectory}
337 echo commonOutputPath ${commonOutputPath}
338 echo doneFile ${doneFile}
339 echo runpath ${runpath}
340 echo outputDir ${outputDir}
341 echo ALICE_ROOT ${ALICE_ROOT}
342 echo PWD ${PWD}
343 echo "########## ###########"
344
345 alirootInfo > ALICE_ROOT.log
346
347 filesCPass1=(
348 "${commonOutputPath}/runCPass1.sh"
349 "${commonOutputPath}/recCPass1.C"
350 "${commonOutputPath}/recCPass1_OuterDet.C"
351 "${commonOutputPath}/runCalibTrain.C"
352 "${commonOutputPath}/QAtrain_duo.C"
353 "${commonOutputPath}/localOCDBaccessConfig.C"
354 "${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz"
355 "${commonOutputPath}/OCDB.root"
356 "${trustedQAtrainMacro}"
357 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/runCPass1.sh"
358 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/recCPass1.C"
359 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/recCPass1_OuterDet.C"
360 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/runCalibTrain.C"
361 "${ALICE_ROOT}/ANALYSIS/macros/QAtrain_duo.C"
362 )
363
364 for file in ${filesCPass1[*]}; do
365 [[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
366 done
367
368 echo "this directory (${PWD}) contents:"
369 /bin/ls
370 echo
371
372 sed -i '/.*root .*\.C/ s|\s*,\s*|,|g' *.sh
373
374 if [[ -n ${postSetUpActionCPass1} ]]; then
375 echo "running ${postSetUpActionCPass1}"
376 eval ${postSetUpActionCPass1}
377 echo
378 fi
379
380 #configure local OCDB storage from CPass0 (creates the localOCDBaccessConfig.C script)
381 if [[ -f cpass0.localOCDB.${runNumber}.tgz ]]; then
382 echo goMakeLocalOCDBaccessConfig "cpass0.localOCDB.${runNumber}.tgz"
383 goMakeLocalOCDBaccessConfig "cpass0.localOCDB.${runNumber}.tgz"
384 else
385 echo "WARNING: file cpass0.localOCDB.${runNumber}.tgz not found!"
386 fi
387
388 if [[ ! $(/bin/ls -1 OCDB/*/*/*/*.root 2>/dev/null) ]]; then
389 echo "cpass0 produced no calibration! exiting..."
390 touch ${doneFile}
391 return 1
392 fi
393
394 #create the Barrel and OuterDet directories for CPass1 and link the local OCDB directory
395 #there to make the localOCDBaccessConfig.C file work, since it may point to the OCDB
396 #entries using a relative path, e.g. local://./OCDB
397 mkdir Barrel OuterDet
398 ln -s ../OCDB Barrel/OCDB
399 ln -s ../OCDB OuterDet/OCDB
400
401 #setup the filtering
402 #the following option enables the filtering task inside the QAtrain_duo.C
403 [[ -n $runESDfiltering ]] && export QA_TaskFilteredTree=1
404 #set the downscaling factors during the filtering fro expert QA (overrides the previous values)
405 if [[ -n ${filteringFactorHighPt} ]]; then
406 export AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF=${filteringFactorHighPt}
407 fi
408 if [[ -n ${filteringFactorV0s} ]]; then
409 export AliAnalysisTaskFilteredTree_fLowPtV0DownscaligF=${filteringFactorV0s}
410 fi
411
412 #run CPass1
413 chmod u+x runCPass1.sh
414 echo "${runpath}/runCPass1.sh ${infile} ${nEvents} ${runNumber} ${ocdbPath} ${recoTriggerOptions}"
415 if [[ -n ${pretend} ]]; then
416 touch AliESDs_Barrel.root
417 touch AliESDfriends_Barrel.root
418 touch AliESDfriends_v1.root
419 touch QAresults_barrel.root
420 touch EventStat_temp_barrel.root
421 touch AODtpITS.root
422 touch AliESDs_Outer.root
423 touch AliESDfriends_Outer.root
424 touch QAresults_outer.root
425 touch EventStat_temp_outer.root
426 touch rec.log
427 touch calib.log
428 touch qa.log
429 touch filtering.log FilterEvents_Trees.root
430 else
431 ./runCPass1.sh "${infile}" "${nEvents}" "${runNumber}" "${ocdbPath}" "${recoTriggerOptions}"
432
433 [[ ! -f AliESDs_Barrel.root && -f Barrel/AliESDs.root ]] && mv Barrel/AliESDs.root AliESDs_Barrel.root
434 [[ ! -f AliESDfriends_Barrel.root && -f Barrel/AliESDfriends.root ]] && mv Barrel/AliESDfriends.root AliESDfriends_Barrel.root
435 [[ ! -f AliESDfriends_v1.root && -f Barrel/AliESDfriends_v1.root ]] && mv Barrel/AliESDfriends_v1.root .
436 [[ ! -f QAresults_barrel.root && -f Barrel/QAresults_barrel.root ]] && mv Barrel/QAresults_barrel.root .
437 [[ ! -f AliESDs_Outer.root && -f OuterDet/AliESDs.root ]] && mv OuterDet/AliESDs.root AliESDs_Outer.root
438 [[ ! -f AliESDfriends_Outer.root && -f OuterDet/AliESDfriends.root ]] && mv OuterDet/AliESDfriends.root AliESDfriends_Outer.root
439 [[ ! -f QAresults_outer.root && -f OuterDet/QAresults_outer.root ]] && mv OuterDet/QAresults_outer.root .
440 [[ ! -f FilterEvents_Trees.root && -f Barrel/FilterEvents_Trees.root ]] && mv Barrel/FilterEvents_Trees.root .
441
442 #make the filtered tree (if requested and not already produced by QA
443 [[ -f AliESDs_Barrel.root ]] && echo "AliESDs_Barrel.root" > filtered.list
444 if [[ -n ${runESDfiltering} && ! -f FilterEvents_Trees.root ]]; then
445 goMakeFilteredTrees ${PWD} ${runNumber} "filtered.list" ${filteringFactorHighPt} ${filteringFactorV0s} ${ocdbPath} 1000000 0 10000000 0 ${configFile} AliESDs_Barrel.root "${extraOpts[@]}"
446 fi
447
448 fi
449
450 ##handle possible crashes in QA (happens often in trunk)
451 ##rerun QA with a trusted aliroot version
452 #if [[ $(validateLog qa_barrel.log) ]]; then
453 # echo "qa_barrel.log not validated!"
454 #fi
455 #if [[ ! -f QAresults_barrel.root && -f ${setupTrustedAliROOTenvInCurrentShell} || $(validateLog qa_barrel.log) ]]; then
456 # echo "WARNING: using trusted QA aliroot ${ALICE_ROOT}"
457 # source ${setupTrustedAliROOTenvInCurrentShell}
458 # cd Barrel
459 # rm QAresults_barrel.root
460 # rm EventStat_temp_barrel.root
461 # rm AODtpITS.root
462 # [[ ! -f AliESDs.root ]] && ln -s ../AliESDs_Barrel.root AliESDs.root
463 # [[ ! -f AliESDfriends.root ]] && ln -s ../AliESDfriends_Barrel.root AliESDfriends.root
464 # if [[ -n ${trustedQAtrainMacro} ]]; then
465 # eval "cp ${trustedQAtrainMacro} QAtrain_duo_trusted.C"
466 # fi
467 # echo executing aliroot -b -q "QAtrain_duo_trusted.C(\"_barrel\",${runNumber},\"wn.xml\",0,\"${ocdbPath}\")"
468 # time aliroot -b -q "QAtrain_duo.C(\"_barrel\",${runNumber},\"wn.xml\",0,\"${ocdbPath}\")" &> ../qa_barrel_trusted.log
469 # cd ../
470 #fi
471
472 #move stuff to final destination
473 echo "this directory (${PWD}) contents:"
474 /bin/ls
475 echo rm -f ./${chunkName}
476 rm -f ./${chunkName}
477 echo "cp --recursive ${runpath}/* ${outputDir}"
478 cp -pf --recursive ${runpath}/* ${outputDir}
479 echo
480
481 #validate CPass1
482 cd ${outputDir}
483 touch ${doneFile}
484 echo "dir ${outputDir}" >> ${doneFile}
485 if summarizeLogs >> ${doneFile}; then
486 [[ -f AliESDs_Barrel.root ]] && echo "esd ${outputDir}/AliESDs_Barrel.root" >> ${doneFile}
487 [[ -f AliESDfriends_v1.root ]] && echo "calibfile ${outputDir}/AliESDfriends_v1.root" >> ${doneFile}
488 [[ -f QAresults_Barrel.root ]] && echo "qafile ${outputDir}/QAresults_Barrel.root" >> ${doneFile}
489 [[ -f QAresults_Outer.root ]] && echo "qafile ${outputDir}/QAresults_Outer.root" >> ${doneFile}
490 [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
491 fi
492
493 [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
494 return 0
495}
496
497
498goMergeCPass0()
499{
500 #
501 # find the output files and merge them
502 #
503
504 outputDir=${1}
505 ocdbStorage=${2}
506 configFile=${3}
507 runNumber=${4}
508 calibrationFilesToMerge=${5} #can be a non-existent file, will then be produced on the fly
509 shift 5
510 if ! parseConfig ${configFile} "$@"; then return 1; fi
511
512 [[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
513 doneFile="${commonOutputPath}/meta/merge.cpass0.run${runNumber}.done"
514
515 umask 0002
516 ulimit -c unlimited
517
518 [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
519
520 #runpath=${PWD}/rundir_cpass0_Merge_${runNumber}
521 runpath=${outputDir}
522 [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
523 [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
524
525 mkdir -p ${runpath}
526 [[ ! -d ${runpath} ]] && echo "not able to make the runpath ${runpath}" && touch ${doneFile} && return 1
527 cd ${runpath}
528
529 logOutputDir=${runpath}
530 [[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
531 [[ -z ${dontRedirectStdOutToLog} ]] && exec &> ${logOutputDir}/mergeMakeOCDB.log
532 echo "${0} $*"
533
534 mergingScript="mergeMakeOCDB.byComponent.sh"
535
536 echo goMergeCPass0 SETUP:
537 echo runNumber=${runNumber}
538 echo outputDir=${outputDir}
539 echo ocdbStorage=${ocdbStorage}
540 echo calibrationFilesToMerge=${calibrationFilesToMerge}
541 echo mergingScript=${mergingScript}
542 echo commonOutputPath=${commonOutputPath}
543 echo runpath=${runpath}
544
545 # copy files in case they are not already there
546 filesMergeCPass0=(
547 "${commonOutputPath}/${calibrationFilesToMerge}"
548 "${commonOutputPath}/OCDB.root"
549 "${commonOutputPath}/localOCDBaccessConfig.C"
550 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/mergeMakeOCDB.byComponent.sh"
551 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/mergeByComponent.C"
552 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/makeOCDB.C"
553 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/merge.C"
554 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/mergeMakeOCDB.sh"
555 )
556 for file in ${filesMergeCPass0[*]}; do
557 [[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
558 done
559
560 sed -i '/.*root .*\.C/ s|\s*,\s*|,|g' *.sh
561
562 alirootInfo > ALICE_ROOT.log
563
564 #
565 echo "PWD"
566 /bin/ls
567 echo "PWD/.."
568 /bin/ls ../
569
570
571 #merge calibration
572 chmod u+x ${mergingScript}
573 mkdir -p ./OCDB
574 if [[ ! -f ${calibrationFilesToMerge} ]]; then
575 echo "/bin/ls -1 ${outputDir}/*/AliESDfriends_v1.root > ${calibrationFilesToMerge}"
576 /bin/ls -1 ${outputDir}/*/AliESDfriends_v1.root 2>/dev/null > ${calibrationFilesToMerge}
577 fi
578
579 echo "${mergingScript} ${calibrationFilesToMerge} ${runNumber} local://./OCDB ${ocdbStorage}"
580 if [[ -n ${pretend} ]]; then
581 touch CalibObjects.root
582 touch ocdb.log
583 touch merge.log
584 mkdir -p ./OCDB/TPC/Calib/TimeGain/
585 mkdir -p ./OCDB/TPC/Calib/TimeDrift/
586 touch ./OCDB/TPC/Calib/TimeGain/someCalibObject_0-999999_cpass0.root
587 touch ./OCDB/TPC/Calib/TimeDrift/otherCalibObject_0-999999_cpass0.root
588 else
589 ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" ${ocdbStorage}
590 fi
591
592 ### produce the output
593 #tar the produced OCDB for reuse
594 tar czf ${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz ./OCDB
595
596 #produce the calib trees for expert QA (dcsTime.root)
597 goMakeLocalOCDBaccessConfig ./OCDB
598 echo aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
599 aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
600
601 /bin/ls
602
603 #copy all to output dir
604 cp -pf --recursive ${runpath}/* ${outputDir}
605
606 if [[ -n ${generateMC} ]]; then
607 goPrintValues sim ${commonOutputPath}/meta/sim.run${runNumber}.list ${commonOutputPath}/meta/cpass0.job*.run${runNumber}.done
608 fi
609
610 #validate merging cpass0
611 cd ${outputDir}
612 touch ${doneFile}
613 echo "dir ${outputDir}" >> ${doneFile}
614 if summarizeLogs >> ${doneFile}; then
615 [[ -f CalibObjects.root ]] && echo "calibfile ${outputDir}/CalibObjects.root" >> ${doneFile}
616 [[ -f dcsTime.root ]] && echo "dcsTree ${outputDir}/dcsTime.root" >> ${doneFile}
617 fi
618
619 [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
620 return 0
621}
622
623goMergeCPass1()
624{
625 #
626 # find the output files and merge them
627 #
628
629 outputDir=${1}
630 ocdbStorage=${2}
631 configFile=${3}
632 runNumber=${4}
633 calibrationFilesToMerge=${5}
634 qaFilesToMerge=${6}
635 filteredFilesToMerge=${7}
636 shift 7
637 if ! parseConfig ${configFile} "$@"; then return 1; fi
638
639 [[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
640 doneFile="${commonOutputPath}/meta/merge.cpass1.run${runNumber}.done"
641
642 umask 0002
643 ulimit -c unlimited
644
645 #clean up first:
646 rm -f ${outputDir}/*.log
647 rm -f ${outputDir}/*.root
648 rm -f ${outputDir}/*done
649
650 [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
651
652 #runpath=${PWD}/rundir_cpass1_Merge_${runNumber}
653 runpath=${outputDir}
654 [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
655 [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
656
657 mkdir -p ${runpath}
658 [[ ! -d ${runpath} ]] && echo "not able to make the runpath ${runpath}" && touch ${doneFile} && return 1
659 cd ${runpath}
660
661 logOutputDir=${runpath}
662 [[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
663 [[ -z ${dontRedirectStdOutToLog} ]] && exec &> ${logOutputDir}/mergeMakeOCDB.log
664 echo "${0} $*"
665
666 calibrationOutputFileName='AliESDfriends_v1.root'
667 qaOutputFileName='QAresults*.root'
668 mergingScript="mergeMakeOCDB.byComponent.sh"
669 #important to have the string "Stage.txt" in the filename to trigger the merging
670 #it has to be a list of directories containing the files
671 qaMergedOutputFileName="QAresults_merged.root"
672
673 echo goMergeCPass1 SETUP:
674 echo runNumber=${runNumber}
675 echo outputDir=${outputDir}
676 echo ocdbStorage=${ocdbStorage}
677 echo calibrationFilesToMerge=$calibrationFilesToMerge
678 echo qaFilesToMerge=$qaFilesToMerge
679 echo calibrationOutputFileName=${calibrationOutputFileName}
680 echo mergingScript=${mergingScript}
681
682 # copy files in case they are not already there
683 filesMergeCPass1=(
684 "${commonOutputPath}/${calibrationFilesToMerge}"
685 "${commonOutputPath}/${qaFilesToMerge}"
686 "${commonOutputPath}/OCDB.root"
687 "${commonOutputPath}/localOCDBaccessConfig.C"
688 "${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz"
689 "${commonOutputPath}/QAtrain_duo.C"
690 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/mergeMakeOCDB.byComponent.sh"
691 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/mergeByComponent.C"
692 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/makeOCDB.C"
693 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/merge.C"
694 "${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/mergeMakeOCDB.sh"
695 "${trustedQAtrainMacro}"
696 "${ALICE_ROOT}/ANALYSIS/macros/QAtrain_duo.C"
697 )
698 for file in ${filesMergeCPass1[*]}; do
699 [[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
700 done
701
702 sed -i '/.*root .*\.C/ s|\s*,\s*|,|g' *.sh
703
704 #configure local OCDB storage from CPass0 (creates the localOCDBaccessConfig.C script)
705 if [[ -f cpass0.localOCDB.${runNumber}.tgz ]]; then
706 echo goMakeLocalOCDBaccessConfig "cpass0.localOCDB.${runNumber}.tgz"
707 goMakeLocalOCDBaccessConfig "cpass0.localOCDB.${runNumber}.tgz"
708 else
709 echo "WARNING: file cpass0.localOCDB.${runNumber}.tgz not found!"
710 fi
711
712 alirootInfo > ALICE_ROOT.log
713
714 #
715 /bin/ls
716
717 #merge calibration
718 chmod u+x ${mergingScript}
719 mkdir -p OCDB
720
721 #if not provided, create the lists of files to merge
722 if [[ ! -f ${filteredFilesToMerge} ]]; then
723 echo "/bin/ls -1 ${outputDir}/*/FilterEvents_Trees.root > ${filteredFilesToMerge}"
724 /bin/ls -1 ${outputDir}/*/FilterEvents_Trees.root 2>/dev/null > ${filteredFilesToMerge}
725 fi
726 if [[ ! -f ${calibrationFilesToMerge} ]]; then
727 echo "/bin/ls -1 ${outputDir}/*/AliESDfriends_v1.root > ${calibrationFilesToMerge}"
728 /bin/ls -1 ${outputDir}/*/AliESDfriends_v1.root 2>/dev/null > ${calibrationFilesToMerge}
729 fi
730 if [[ ! -f ${qaFilesToMerge} ]]; then
731 #find the files, but only store the directories (QAtrain_duo.C requires this)
732 echo "/bin/ls -1 ${outputDir}/*/QAresults*.root | while read x; do echo ${x%/*}; done | sort | uniq > ${qaFilesToMerge}"
733 /bin/ls -1 ${outputDir}/*/QAresults*.root | while read x; do echo ${x%/*}; done | sort | uniq > ${qaFilesToMerge}
734 fi
735
736 echo "${mergingScript} ${calibrationFilesToMerge} ${runNumber} local://./OCDB ${ocdbStorage}"
737 if [[ -n ${pretend} ]]; then
738 touch CalibObjects.root
739 touch ocdb.log
740 touch merge.log
741 touch cpass1.localOCDB.${runNumber}.tgz
742 else
743 ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" ${ocdbStorage}
744 fi
745
746 tar czf ${commonOutputPath}/meta/cpass1.localOCDB.${runNumber}.tgz ./OCDB
747
748 #merge QA (and filtered trees)
749 [[ -n ${AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF} ]] && export AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF
750 [[ -n ${AliAnalysisTaskFilteredTree_fLowPtV0DownscaligF} ]] && export AliAnalysisTaskFilteredTree_fLowPtV0DownscaligF
751
752 #echo aliroot -l -b -q "merge.C(\"${qaFilesToMerge}\",\"\",kFALSE,\"${qaMergedOutputFileName}\")"
753 echo aliroot -b -q "QAtrain_duo.C(\"_barrel\",${runNumber},\"${qaFilesToMerge}\",1,\"${ocdbStorage}\")"
754 if [[ -n ${pretend} ]]; then
755 touch ${qaMergedOutputFileName}
756 touch merge.log
757 touch trending.root
758 touch FilterEvents_Trees.root
759 touch CalibObjects.root
760 touch dcsTime.root
761 touch ${qaMergedOutputFileName}
762 else
763 #aliroot -l -b -q "merge.C(\"${qaFilesToMerge}\",\"\",kFALSE,\"${qaMergedOutputFileName}\")"
764 aliroot -b -q "QAtrain_duo.C(\"_barrel\",${runNumber},\"${qaFilesToMerge}\",1,\"${ocdbStorage}\")" > mergeQA.log
765 mv QAresults_barrel.root ${qaMergedOutputFileName}
766 mv trending_barrel.root trending.root
767
768 #merge filtered trees
769 echo aliroot -l -b -q "merge.C(\"${qaFilesToMerge}\",\"\",kFALSE,\"${qaMergedOutputFileName}\")"
770 aliroot -l -b -q "merge.C(\"${filteredFilesToMerge}\",\"\",kFALSE,\"FilterEvents_Trees.root\")"
771 fi
772
773 #produce the calib trees for expert QA
774 echo aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
775 aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
776
777 /bin/ls
778
779 #copy all to output dir
780 cp -pf --recursive ${runpath}/* ${outputDir}
781
782 #validate merge cpass1
783 cd ${outputDir}
784 touch ${doneFile}
785 echo "dir ${outputDir}" >> ${doneFile}
786 if summarizeLogs >> ${doneFile}; then
787 [[ -f CalibObjects.root ]] && echo "calibfile ${outputDir}/CalibObjects.root" >> ${doneFile}
788 [[ -f ${qaMergedOutputFileName} ]] && echo "qafile ${outputDir}/${qaMergedOutputFileName}" >> ${doneFile}
789 [[ -f trending.root ]] && echo "trendingfile ${outputDir}/trending.root" >> ${doneFile}
790 [[ -f dcsTime.root ]] && echo "dcsTree ${outputDir}/dcsTime.root" >> ${doneFile}
791 [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
792 fi
793
794 [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
795 return 0
796}
797
798goMerge()
799{
800 #generic root merge using CPass1 merge.C script
801 inputList=${1}
802 outputFile=${2}
803 configFile=${3-"becnhmark.config"}
804 shift 3
805 if ! parseConfig ${configFile} "$@"; then return 1; fi
806
807 [[ ! -f ${inputList} ]] && echo "inputList ${inputList} does not exist!" && return 1
808 [[ ! -f ${configFile} ]] && echo "configFile ${configFile} does not exist!" && return 1
809 umask 0002
810 [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
811 rm -f ${outputFile}
812 aliroot -b -q "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/merge.C(\"${inputList}\",\"\",kFALSE,\"${outputFile}\")" > merge_${inputList}.log
813 return 0
814}
815
816goSubmitMakeflow()
817{
818 #run
819 productionID=${1}
820 inputFileList=${2}
821 configFile=${3}
822 shift 3
823 extraOpts=("$@")
824 if ! parseConfig ${configFile} "${extraOpts[@]}"; then return 1; fi
825
826 [[ -z ${configFile} ]] && configFile="benchmark.config"
827 [[ ! -f ${configFile} ]] && echo "no config file found (${configFile})" && return 1
828
829 #create the directopry for the metadata
830 mkdir meta
831
832 if [[ ! $(which makeflow &>/dev/null) && -n ${makeflowPath} ]]; then
833 echo "setting the makflow path from the config: "
834 echo " export PATH=${makeflowPath}:${PATH}"
835 export PATH=${makeflowPath}:${PATH}
836 fi
837
838 #submit - use makeflow if available, fall back to old stuff when makeflow not there
839 if which makeflow; then
840
841 goGenerateMakeflow ${productionID} ${inputFileList} ${configFile} "${extraOpts[@]}" > benchmark.makeflow
842
843 makeflow ${makeflowOptions} benchmark.makeflow
844 cd ../
845 else
846 echo "no makeflow!"
847 fi
848 return 0
849}
850
851goGenerateMakeflow()
852{
853 #generate the makeflow file
854 [[ $# -lt 3 ]] && echo "args: id inputFileList configFile" && return 1
855 productionID=${1}
856 inputFileList=${2}
857 configFile=${3}
858 shift 3
859 extraOpts=("$@")
860 if ! parseConfig ${configFile} "${extraOpts[@]}"; then return 1; fi
861
862 [[ -z ${configFile} ]] && configFile="benchmark.config"
863 [[ ! -f ${configFile} ]] && echo "no config file found (${configFile})" && return 1
864
865 commonOutputPath=${baseOutputDirectory}/${productionID}
866
867 self=$(readlink -f "${0}")
868 echo "self: $self"
869 #these files will be made a dependency - will be copied to the working dir of the jobs
870 declare -a copyFiles
871 inputFiles=(
872 "OCDB.root"
873 "localOCDBaccessConfig.C"
874 "QAtrain_duo.C"
875 "runCPass1.sh"
876 "recCPass1.C"
877 "recCPass1_OuterDet.C"
878 "runCalibTrain.C"
879 "runCPass0.sh"
880 "recCPass0.C"
881 )
882 for file in ${inputFiles[*]}; do
883 [[ -f ${file} ]] && copyFiles+=("${file}")
884 done
885
886 #create the makeflow file
887 [[ -n ${batchFlags} ]] && echo "BATCH_OPTIONS = ${batchFlags}"
888 declare -A arr_cpass0_merged arr_cpass1_merged
889 declare -A arr_cpass0_calib_list arr_cpass1_calib_list
890 declare -A arr_cpass1_QA_list arr_cpass1_ESD_list arr_cpass1_filtered_list
891 declare -A arr_cpass0_profiled_outputs
892 declare -A listOfRuns
893 [[ -n ${runNumber} ]] && listOfRuns[${runNumber}]=1
894 while read x; do listOfRuns[$(guessRunNumber ${x})]=1; done < ${inputFileList}
895 for runNumber in "${!listOfRuns[@]}"; do
896 [[ -z ${runNumber} ]] && continue
897 [[ ! ${runNumber} =~ ^[0-9]*[0-9]$ ]] && continue
898
899 unset arr_cpass0_outputs
900 unset arr_cpass1_outputs
901 declare -a arr_cpass0_outputs
902 declare -a arr_cpass1_outputs
903
904 jobindex=0
905 inputFile=""
906 while read inputFile; do
907 currentDefaultOCDB=${defaultOCDB}
908 [[ -z ${autoOCDB} ]] && autoOCDB=1
909 if [[ ${autoOCDB} -ne 0 ]]; then
910 currentDefaultOCDB=$(setYear ${inputFile} ${defaultOCDB})
911 fi
912
913 #CPass0
914 arr_cpass0_outputs[${jobindex}]="meta/cpass0.job${jobindex}.run${runNumber}.done"
915 echo "${arr_cpass0_outputs[${jobindex}]} : benchmark.sh ${configFile} ${copyFiles[@]}"
916 echo -n " ${alirootEnv} ./benchmark.sh CPass0 ${commonOutputPath}/000${runNumber}/cpass0 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex}"" "
917 for extraOption in "${extraOpts[@]}"; do echo -n \"${extraOption}\"" "; done; echo
918 echo
919
920 #CPass1
921 arr_cpass1_outputs[${jobindex}]="meta/cpass1.job${jobindex}.run${runNumber}.done"
922 echo "${arr_cpass1_outputs[${jobindex}]} : benchmark.sh ${configFile} meta/cpass0.localOCDB.${runNumber}.tgz ${copyFiles[@]}"
923 echo -n " ${alirootEnv} ./benchmark.sh CPass1 ${commonOutputPath}/000${runNumber}/cpass1 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex}"" "
924 for extraOption in "${extraOpts[@]}"; do echo -n \"${extraOption}\"" "; done; echo
925 echo
926 ((jobindex++))
927
928 done< <(grep "/000${runNumber}/" ${inputFileList})
929
930 #CPass0 list of Calib files to merge
931 arr_cpass0_calib_list[${runNumber}]="meta/cpass0.calib.run${runNumber}.list"
932 echo "${arr_cpass0_calib_list[${runNumber}]} : benchmark.sh ${arr_cpass0_outputs[*]}"
933 echo " ./benchmark.sh PrintValues calibfile ${arr_cpass0_calib_list[${runNumber}]} ${arr_cpass0_outputs[*]}"
934 echo
935
936 #CPass0 merging
937 arr_cpass0_merged[${runNumber}]="meta/merge.cpass0.run${runNumber}.done"
938 echo "meta/cpass0.localOCDB.${runNumber}.tgz ${arr_cpass0_merged[${runNumber}]} : benchmark.sh ${configFile} ${arr_cpass0_calib_list[${runNumber}]} ${copyFiles[@]}"
939 echo -n " ${alirootEnv} ./benchmark.sh MergeCPass0 ${commonOutputPath}/000${runNumber}/cpass0 ${currentDefaultOCDB} ${configFile} ${runNumber} ${arr_cpass0_calib_list[${runNumber}]}"" "
940 for extraOption in "${extraOpts[@]}"; do echo -n \"${extraOption}\"" "; done; echo
941 echo
942
943 #CPass1 list of Calib/QA/ESD/filtered files
944 # the trick with QA is to have the string "Stage.txt" in the file name of the list of directories with QA output to trigger
945 # the production of the QA trending tree (only then the task->Finish() will be called in QAtrain_duo.C, on the grid
946 # this corresponds to the last merging stage)
947 arr_cpass1_QA_list[${runNumber}]="meta/cpass1.QA.run${runNumber}.lastMergingStage.txt.list"
948 echo "${arr_cpass1_QA_list[${runNumber}]}: benchmark.sh ${arr_cpass1_outputs[*]}"
949 echo " ./benchmark.sh PrintValues dir ${arr_cpass1_QA_list[${runNumber}]} ${arr_cpass1_outputs[*]}"
950 echo
951 arr_cpass1_calib_list[${runNumber}]="meta/cpass1.calib.run${runNumber}.list"
952 echo "${arr_cpass1_calib_list[${runNumber}]} : benchmark.sh ${arr_cpass1_outputs[*]}"
953 echo " ./benchmark.sh PrintValues calibfile ${arr_cpass1_calib_list[${runNumber}]} ${arr_cpass1_outputs[*]};"
954 echo
955 arr_cpass1_ESD_list[${runNumber}]="meta/cpass1.ESD.run${runNumber}.list"
956 echo "${arr_cpass1_ESD_list[${runNumber}]} : benchmark.sh ${arr_cpass1_outputs[*]}"
957 echo " ./benchmark.sh PrintValues esd ${arr_cpass1_ESD_list[${runNumber}]} ${arr_cpass1_outputs[*]}"
958 echo
959 arr_cpass1_filtered_list[${runNumber}]="meta/cpass1.filtered.run${runNumber}.list"
960 echo "${arr_cpass1_filtered_list[${runNumber}]} : benchmark.sh ${arr_cpass1_outputs[*]}"
961 echo " ./benchmark.sh PrintValues filteredTree ${arr_cpass1_filtered_list[${runNumber}]} ${arr_cpass1_outputs[*]}"
962 echo
963
964 #CPass1 merging
965 arr_cpass1_merged[${runNumber}]="meta/merge.cpass1.run${runNumber}.done"
966 echo "meta/cpass1.localOCDB.${runNumber}.tgz ${arr_cpass1_merged[${runNumber}]} : benchmark.sh ${configFile} ${arr_cpass1_calib_list[${runNumber}]} ${arr_cpass1_QA_list[${runNumber}]} ${copyFiles[@]}"
967 echo -n " ${alirootEnv} ./benchmark.sh MergeCPass1 ${commonOutputPath}/000${runNumber}/cpass1 ${currentDefaultOCDB} ${configFile} ${runNumber} ${arr_cpass1_calib_list[${runNumber}]} ${arr_cpass1_QA_list[${runNumber}]} ${arr_cpass1_filtered_list[${runNumber}]}"" "
968 for extraOption in "${extraOpts[@]}"; do echo -n \"${extraOption}\"" "; done; echo
969 echo
970
971 #CPass0 wrapped in a profiling tool (valgrind,....)
972 if [[ -n profilingCommand ]]; then
973 arr_cpass0_profiled_outputs[${runNumber}]="meta/cpass0.jobProfiled.run${runNumber}.done"
974 echo "${arr_cpass0_profiled_outputs[${runNumber}]} : benchmark.sh ${configFile} ${copyFiles[@]}"
975 echo -n " ${alirootEnv} ./benchmark.sh CPass0 ${commonOutputPath}/000${runNumber}/profiled ${inputFile} ${nEventsProfiling} ${currentDefaultOCDB} ${configFile} ${runNumber} profiling"" "
976 for extraOption in "${extraOpts[@]}"; do echo -n \"${extraOption}\"" "; done;
977 echo "\"useProfilingCommand=${profilingCommand}\""
978 echo
979 fi
980
981 done #runs
982
983 #Summary
984 echo "summary.log : benchmark.sh ${configFile} ${arr_cpass1_merged[*]}"
985 echo " LOCAL ./benchmark.sh MakeSummary ${configFile}"
986 echo
987
988 return 0
989}
990
991goPrintValues()
992{
993 #print the values given the key from any number of files (store in output file on second argument)
994 if [[ $# -lt 3 ]]; then
995 echo "goPrintValues key outputFile inputFiles"
996 echo "if outputFile is \"-\" dont redirect to a file"
997 return
998 fi
999 key=${1}
1000 outputFile=${2}
1001 [[ ${outputFile} =~ "-" ]] && outputFile=""
1002 shift 2 #remove 2 first arguments from arg list to only pass the input files to awk
1003 awk -v key=${key} '$0 ~ key" " {print $2}' "$@" | tee ${outputFile}
1004 return 0
1005}
1006
1007goCreateQAplots()
1008{
1009 umask 0002
1010 mergedQAfileList=${1}
1011 productionID=${2}
1012 outputDir=${3}
1013 configFile=${4}
1014 shift 4
1015 if ! parseConfig ${configFile} ${@}; then return 1; fi
1016
1017 [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
1018
1019 [[ -z ${logOutputDir} ]] && logOutputDir=${PWD}
1020 [[ -z ${dontRedirectStdOutToLog} ]] && exec 2>&1 > ${logOutputDir}/makeQAplots.log
1021 echo "${0} $*"
1022
1023 olddir=${PWD}
1024 mkdir -p ${outputDir}
1025 cd ${outputDir}
1026 [[ ! "${PWD}" = "${outputDir}" ]] && echo "cannot make ${outputDir}... exiting" && return 1
1027
1028 echo ${ALICE_ROOT}/PWGPP/QA/scripts/runQA.sh inputList=${mergedQAfileList}
1029 ${ALICE_ROOT}/PWGPP/QA/scripts/runQA.sh inputList="${mergedQAfileList}" inputListHighPtTrees="${filteringList}"
1030
1031 cd ${olddir}
1032 return 0
1033}
1034
1035goTest()
1036{
1037 umask 0002
1038 exec 2>&1
1039 exec > >(tee test.log)
1040 echo "$@"
1041 echo something
1042 return 0
1043}
1044
1045alirootInfo()
1046{
1047 umask 0002
1048 # save aliroot repository info
1049 [[ -z "${ALICE_ROOT}" ]] && return 1
1050
1051 echo "\${ALICE_ROOT}=${ALICE_ROOT}"
1052 echo "\${ROOTSYS}=${ROOTSYS}"
1053 echo "\${PATH}=${PATH}"
1054 echo "\${LD_LIBRARY_PATH}=${LD_LIBRARY_PATH}"
1055
1056 pushd ${PWD}
1057 cd ${ALICE_ROOT}
1058 echo
1059
1060 currentBranch=$(git rev-parse --abbrev-ref HEAD)
1061 git status
1062 echo ""
1063 echo ""
1064 git diff ${currentBranch}
1065 popd
1066 return 0
1067}
1068
1069setYear()
1070{
1071 #set the year
1072 # ${1} - year to be set
1073 # ${2} - where to set the year
1074 year1=$(guessYear ${1})
1075 year2=$(guessYear ${2})
1076 local path=${2}
1077 [[ ${year1} -ne ${year2} && -n ${year2} && -n ${year1} ]] && path=${2/\/${year2}\//\/${year1}\/}
1078 echo ${path}
1079 return 0
1080}
1081
1082guessPeriod()
1083{
1084 #guess the period from the path, pick the rightmost one
1085 local IFS="/"
1086 declare -a path=( ${1} )
1087 local dirDepth=${#path[*]}
1088 for ((x=${dirDepth}-1;x>=0;x--)); do
1089 local field=${path[${x}]}
1090 [[ ${field} =~ ^LHC[0-9][0-9][a-z]$ ]] && period=${field} && break
1091 done
1092 echo ${period}
1093 return 0
1094}
1095
1096guessYear()
1097{
1098 #guess the year from the path, pick the rightmost one
1099 local IFS="/"
1100 declare -a path=( ${1} )
1101 local dirDepth=${#path[*]}
1102 for ((x=${dirDepth}-1;x>=0;x--)); do
1103 local field=${path[${x}]}
1104 [[ ${field} =~ ^20[0-9][0-9]$ ]] && year=${field} && break
1105 done
1106 echo ${year}
1107 return 0
1108}
1109
1110guessRunNumber()
1111{
1112 #guess the run number from the path, pick the rightmost one
1113 #works for /path/foo/000123456/bar/...
1114 #and /path/foo.run123456.bar
1115 local IFS="/."
1116 declare -a path=( ${1} )
1117 local dirDepth=${#path[*]}
1118 for ((x=${dirDepth}-1;x>=0;x--)); do
1119 local field=${path[${x}]}
1120 field=${field/run/000}
1121 [[ ${field} =~ ^000[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && runNumber=${field#000} && break
1122 done
1123 echo ${runNumber}
1124 return 0
1125}
1126
1127validateLog()
1128{
1129 log=${1}
1130 errorConditions=(
1131 'There was a crash'
1132 'floating'
1133 'error while loading shared libraries'
1134 'std::bad_alloc'
1135 's_err_syswatch_'
1136 'Thread [0-9]* (Thread'
1137 'AliFatal'
1138 'core dumped'
1139 '\.C.*error:.*\.h: No such file'
1140 )
1141
1142 warningConditions=(
1143 'This is serious !'
1144 'rocVoltage out of range:'
1145 )
1146
1147 local logstatus=0
1148 local errorSummary=""
1149 local warningSummary=""
1150
1151 for ((i=0; i<${#errorConditions[@]};i++)); do
1152 local tmp=$(grep -m1 -e "${errorConditions[${i}]}" ${log})
1153 [[ -n ${tmp} ]] && tmp+=" : "
1154 errorSummary+=${tmp}
1155 done
1156
1157 for ((i=0; i<${#warningConditions[@]};i++)); do
1158 local tmp=$(grep -m1 -e "${warningConditions[${i}]}" ${log})
1159 [[ -n ${tmp} ]] && tmp+=" : "
1160 warningSummary+=${tmp}
1161 done
1162
1163 if [[ -n ${errorSummary} ]]; then
1164 echo "${errorSummary}"
1165 return 1
1166 fi
1167
1168 if [[ -n ${warningSummary} ]]; then
1169 echo "${warningSummary}"
1170 return 2
1171 fi
1172
1173 return 0
1174}
1175
1176summarizeLogs()
1177{
1178 #print a summary of logs
1179 logFiles=(
1180 "*.log"
1181 "stdout"
1182 "stderr"
1183 )
1184
1185 #check logs
1186 local logstatus=0
1187 for log in ${logFiles[*]}; do
1188 finallog=${PWD%/}/${log}
1189 [[ ! -f ${log} ]] && continue
1190 errorSummary=$(validateLog ${log})
1191 validationStatus=$?
1192 if [[ ${validationStatus} -eq 0 ]]; then
1193 #in pretend mode randomly report an error in rec.log some cases
1194 if [[ -n ${pretend} && "${log}" == "rec.log" ]]; then
1195 [[ $(( ${RANDOM}%2 )) -ge 1 ]] && echo "${finallog} BAD random error" || echo "${finallog} OK"
1196 else
1197 echo "${finallog} OK"
1198 fi
1199 elif [[ ${validationStatus} -eq 1 ]]; then
1200 echo "${finallog} BAD ${errorSummary}"
1201 logstatus=1
1202 elif [[ ${validationStatus} -eq 2 ]]; then
1203 echo "${finallog} OK MWAH ${errorSummary}"
1204 fi
1205 done
1206
1207 #report core files
1208 while read x; do
1209 echo ${x}
1210 chmod 644 ${x}
1211 gdb --batch --quiet -ex "bt" -ex "quit" aliroot ${x} > stacktrace_${x//\//_}.log
1212 done < <(/bin/ls ${PWD}/*/core 2>/dev/null; /bin/ls ${PWD}/core 2>/dev/null)
1213
1214 return ${logstatus}
1215}
1216
1217spitOutLocalOCDBaccessConfig()
1218{
1219 umask 0002
1220 #find ${1} -name "*root" | \
1221 /bin/ls -1 ${1}/*/*/*/*.root 2>/dev/null | \
1222 while read line
1223 do
1224 local tmp=${line#${1}}
1225 echo ${tmp%/*} | \
1226 awk -v ocdb=${1} '{print " man->SetSpecificStorage(\""$1"\",\"local://"ocdb"\");"}'
1227 done
1228 return 0
1229}
1230
1231goMakeLocalOCDBaccessConfig()
1232{
1233 umask 0002
1234 # make a script that sets the specific storages form all the root files produced by CPass0
1235 local localOCDBpathCPass0=${1}
1236 local OCDBpathPrefix=${2}
1237 [[ -z ${OCDBpathPrefix} ]] && OCDBpathPrefix="."
1238
1239 if [[ -f ${localOCDBpathCPass0} && ${localOCDBpathCPass0} =~ \.tgz$ ]]; then
1240 tar xzf ${localOCDBpathCPass0}
1241 local localOCDBpathCPass0="${OCDBpathPrefix}/OCDB"
1242 fi
1243
1244 echo
1245 echo creating the specific storage script
1246 echo localOCDBaccessConfig.C
1247 echo based on OCDB: ${localOCDBaccessConfig}
1248 echo
1249
1250 local tempLocalOCDB=""
1251 if [[ -f localOCDBaccessConfig.C ]]; then
1252 tempLocalOCDB=$(mktemp)
1253 echo "egrep "SetSpecificStorage" localOCDBaccessConfig.C > ${tempLocalOCDB}"
1254 egrep "SetSpecificStorage" localOCDBaccessConfig.C > ${tempLocalOCDB}
1255 fi
1256
1257 echo "localOCDBaccessConfig()" > localOCDBaccessConfig.C
1258 echo "{" >> localOCDBaccessConfig.C
1259 echo " AliCDBManager* man = AliCDBManager::Instance();" >> localOCDBaccessConfig.C
1260 spitOutLocalOCDBaccessConfig ${localOCDBpathCPass0}|sort|uniq >> localOCDBaccessConfig.C
1261 [[ -f "${tempLocalOCDB}" ]] && cat ${tempLocalOCDB} >> localOCDBaccessConfig.C
1262 echo "}" >> localOCDBaccessConfig.C
1263
1264 [[ -f "${tempLocalOCDB}" ]] && rm -f ${tempLocalOCDB}
1265
1266 if ! grep SetSpecificStorage localOCDBaccessConfig.C; then
1267 echo
1268 echo "!!!!!!! CPass0 produced no OCDB entries"
1269 return 1
1270 fi
1271 return 0
1272}
1273
1274goMakeFilteredTrees()
1275{
1276 outputDir=${1}
1277 runNumber=${2}
1278 #get path to input list
1279 inputListfiles=${3}
1280 #get scale number for tracks
1281 filterT=${4}
1282 #get scale number for V0s
1283 filterV=${5}
1284 #get OCDB path (optional)
1285 OCDBpath=${6}
1286 #get max number of files
1287 maxFiles=${7-"1000000"}
1288 #get offset of first file
1289 offsetFile=${8-"0"}
1290 #get max number of events
1291 maxEvents=${9-"30000000"}
1292 #get offset of first event
1293 offsetEvent=${10-"0"}
1294 configFile=${11-"benchmark.config"}
1295 esdFileName=${12-"AliESDs_Barrel.root"}
1296 shift 12
1297 if ! parseConfig ${configFile} "$@"; then return 1; fi
1298
1299 commonOutputPath=${PWD}
1300 doneFile=${commonOutputPath}/meta/filtering.cpass1.run${runNumber}.done
1301
1302 runpath=${outputDir}
1303 [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
1304 [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
1305
1306
1307 [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
1308
1309 mkdir -p ${outputDir}
1310 mkdir -p ${runpath}
1311
1312 cd ${runpath}
1313
1314 cat > filtering.log << EOF
1315 goMakeFilteredTrees config:
1316 runpath=${runpath}
1317 outputDir=${outputDir}
1318 commonOutputPath=${commonOutputPath}
1319 ALICE_ROOT=${ALICE_ROOT}
1320 PATH=${PATH}
1321 offsetEvent=$offsetEvent
1322 configFile=$configFile
1323 esdFileName=$esdFileName
1324EOF
1325
1326 if [[ -z ${pretend} ]];then
1327 aliroot -l -b -q "${ALICE_ROOT}/PWGPP/macros/runFilteringTask.C(\"${inputListfiles}\",${filterT},${filterV},\"${OCDBpath}\",${maxFiles},${offsetFile},${maxEvents},${offsetEvent},\"${esdFileName}\")" &>> filtering.log
1328 else
1329 touch filtering.log FilterEvents_Trees.root
1330 fi
1331 pwd
1332 /bin/ls
1333 touch ${doneFile}
1334 summarizeLogs >> ${doneFile}
1335 echo mv -f * ${outputDir}
1336 mv -f * ${outputDir}
1337 [[ -f ${outputDir}/FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
1338 cd ${commonOutputPath}
1339 [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
1340 return 0
1341}
1342
1343submit()
1344{
1345 umask 0002
1346 [[ $# -lt 5 ]] && echo "at least 5 args needed, you supplied $#" && return 1
1347 JobID=${1}
1348 startID=${2}
1349 endID=${3}
1350 waitForJOBID=${4}
1351 command=${5}
1352 shift 5
1353 commandArgs=("$@")
1354
1355 #add quote strings around the extra arguments
1356 for ((i=0; i<${#commandArgs[@]}; i++)); do
1357 commandArgs[i]=\"${commandArgs[i]}\"
1358 done
1359
1360 [[ -z ${waitForJOBID} ]] && waitForJOBID=0
1361
1362 newFarm=$(which qsub|grep "^/usr/bin/qsub")
1363
1364 batchSystem="SGE"
1365
1366 if [[ -z "${newFarm}" ]]
1367 then
1368 #old LSF
1369 # submit it (as job array)
1370 nFiles=$(( ${endID}-${startID}+1 ))
1371 while [ ${startID} -le ${nFiles} ] ; do
1372 if [ $(expr ${nFiles} - ${startID}) -gt 999 ] ; then
1373 endID=$(expr ${startID} + 999)
1374 else
1375 endID=${nFiles}
1376 fi
1377 if [[ ${waitForJOBID} -eq 0 ]]; then
1378 echo ${batchCommand} ${batchFlags} -J "${JobID}[${startID}-${endID}]" -e "${commonOutputPath}/logs/job_%I.err" -o "${commonOutputPath}/logs/job_%I.out" "${command}"
1379 ${batchCommand} ${batchFlags} -J "${JobID}[${startID}-${endID}]" -e "${commonOutputPath}/logs/job_%I.err" -o "${commonOutputPath}/logs/job_%I.out" "${command}"
1380 else
1381 echo ${batchCommand} ${batchFlags} -J "${JobID}[${startID}-${endID}]" -w "ended(${waitForJOBID})" -e "${commonOutputPath}/logs/job_%I.err" -o "${commonOutputPath}/logs/job_%I.out" "${command}"
1382 ${batchCommand} ${batchFlags} -J "${JobID}[${startID}-${endID}]" -w "ended(${waitForJOBID})" -e "${commonOutputPath}/logs/job_%I.err" -o "${commonOutputPath}/logs/job_%I.out" "${command}"
1383 fi
1384 startID=$(expr ${endID} + 1)
1385 done
1386 else
1387 #new SGE farm
1388 if [[ ${waitForJOBID} =~ "000" ]]; then
1389 echo ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" "${commandArgs[@]}"
1390 ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" "${commandArgs[@]}"
1391 else
1392 echo ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -hold_jid "${waitForJOBID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" "${commandArgs[@]}"
1393 ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -hold_jid "${waitForJOBID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" "${commandArgs[@]}"
1394 fi
1395 fi
1396 return 0
1397}
1398
1399goSubmitBatch()
1400{
1401 if [[ $# -lt 3 ]]; then
1402 echo "minimal use:"
1403 echo " ${0} submit fileList productionID configFile"
1404 return 0
1405 fi
1406
1407 productionID=${1}
1408 inputList=${2}
1409 configFile=${3:-"benchmark.config"}
1410 configFile=$(readlink -f ${configFile})
1411 shift 3
1412 extraOpts=("$@")
1413 if ! parseConfig ${configFile} "${extraOpts[@]}"; then return 1; fi
1414
1415 #redirect all output to submit.log
1416 echo "redirecting all output to ${PWD}/submit_${productionID//"/"/_}.log"
1417 exec 7>&1
1418 exec 1>submit_${productionID//"/"/_}.log 2>&1
1419
1420 umask 0002
1421 echo ${0}" submit $*"
1422 if [[ -z "${inputList}" || -z "${productionID}" ]]
1423 then
1424 echo
1425 echo " Usage: ${0} submit inputList productionID [configFile=benchmark.config]"
1426 echo
1427 return
1428 fi
1429
1430 # check if config file is there
1431 if [ ! -f ${configFile} ]; then
1432 echo "ERROR! Config File '${configFile}' not found" >&2
1433 return
1434 else
1435 echo "Using Config File: '${configFile}'"
1436 fi
1437
1438 [[ ! -f ${alirootEnv} ]] && echo "alirootEnv script ${alirootEnv} not found!..." && return 1
1439
1440 #move the script, config and some other stuff to ${commonOutputPath} first, then use them from there
1441 self=$(readlink -f "${0}")
1442 configPath=$(dirname ${configFile})
1443 export commonOutputPath=${baseOutputDirectory}/${productionID}
1444
1445 mkdir -p ${commonOutputPath}
1446 mkdir -p ${commonOutputPath}/logs
1447 mkdir -p ${commonOutputPath}/meta
1448
1449 cp ${self} ${commonOutputPath}
1450 cp ${configFile} ${commonOutputPath}
1451 cp ${inputList} ${commonOutputPath}
1452 self=${commonOutputPath}/${self##*/}
1453 chmod u+x ${self}
1454 configFile=${commonOutputPath}/${configFile##*/}
1455 inputList=${commonOutputPath}/${inputList##*/}
1456
1457 #convert to absolut pathnames
1458 inputList=$(readlink -f "${inputList}")
1459 #make list of runs
1460 if [[ -z ${runNumber} ]]; then
1461 listOfRuns=($(while read x; do guessRunNumber ${x}; done < ${inputList} | sort | uniq))
1462 else
1463 listOfRuns=${runNumber}
1464 fi
1465
1466 alirootSource=$(readlink -f "${alirootSource}")
1467
1468 echo ""
1469 echo "### BEGIN CONFIGURATION ###"
1470 echo ""
1471 echo "GENERAL:"
1472 echo ""
1473 echo " productionID: ${productionID}"
1474 echo " batchCommand: ${batchCommand}"
1475 echo " batchFlags: ${batchFlags}"
1476 echo " alirootEnv: ${alirootEnv}"
1477 ${alirootEnv} echo ' ALICE_ROOT: ${ALICE_ROOT}'
1478 ${alirootEnv} echo ' ALIROOT_RELEASE: ${ALICE_RELEASE}'
1479 echo " inputList: ${inputList}"
1480 echo " configPath: ${configPath}"
1481 echo " commonOutputPath: ${commonOutputPath}"
1482 echo " defaultOCDB: ${defaultOCDB}"
1483 echo " autoOCDB: ${autoOCDB}"
1484 echo " recoTriggerOptions: ${recoTriggerOptions}"
1485 echo " runs:"
1486 echo " ${listOfRuns[*]}"
1487 echo ""
1488 echo "THE TRAIN WILL RUN:"
1489
1490 if [ ${runCPass0reco} -eq 1 ]; then
1491 echo " Pass0 - Recontruction"
1492 fi
1493
1494 if [ ${runCPass0MergeMakeOCDB} -eq 1 ]; then
1495 echo " Pass0 - merging and OCDB export"
1496 fi
1497
1498 if [ ${runCPass1reco} -eq 1 ]; then
1499 echo " Pass1 - Recontruction"
1500 fi
1501 if [ ${runCPass1MergeMakeOCDB} -eq 1 ]; then
1502 echo " Pass1 - merging and OCDB export"
1503 fi
1504
1505 echo ""
1506 echo "LIMITS:"
1507 echo " max. Events/Chunk: ${nEvents}"
1508 echo " max. Number of Chunks per Run: ${nMaxChunks}"
1509 echo ""
1510 echo "### END CONFIGURATION ###"
1511 echo ""
1512
1513
1514 # check if input file is there
1515 if [ ! -f ${inputList} ]; then
1516 echo "ERROR! Input List '${inputList}' not found" >&2
1517 return
1518 fi
1519
1520 # define jobid (for dependent jobs)
1521 date=$(date +%Y_%m_%d_%H%M%S)
1522 #for each run we submit one jobarray:
1523 for runNumber in ${listOfRuns[*]}; do
1524
1525 [[ -z ${runNumber} ]] && continue
1526 [[ ! ${runNumber} =~ ^[0-9]*[0-9]$ ]] && continue
1527
1528 JOBpostfix="${productionID//"/"/_}_${runNumber}_${date}"
1529 JOBID1="p0_${JOBpostfix}"
1530 JOBID1wait="w0_${JOBpostfix}"
1531 JOBID2="m0_${JOBpostfix}"
1532 JOBID2wait="wm0_${JOBpostfix}"
1533 JOBID3="op0_${JOBpostfix}"
1534 JOBID3wait="wop0_${JOBpostfix}"
1535 JOBID4="p1_${JOBpostfix}"
1536 JOBID4wait="w1_${JOBpostfix}"
1537 JOBID5="m1_${JOBpostfix}"
1538 JOBID5wait="wm1_${JOBpostfix}"
1539 JOBID6="s1_${JOBpostfix}"
1540 JOBID6wait="ws1_${JOBpostfix}"
1541 JOBID7="QA_${JOBpostfix}"
1542 JOBmakeESDlistCPass1="lp1_${JOBpostfix}"
1543 JOBfilterESDcpass1="fp1_${JOBpostfix}"
1544 LASTJOB="000"
1545
1546 oneInputFile=$(egrep -m1 "${runNumber}\/" ${inputList})
1547
1548 currentDefaultOCDB=${defaultOCDB}
1549 [[ -z ${autoOCDB} ]] && autoOCDB=1
1550 if [[ ${autoOCDB} -ne 0 ]]; then
1551 currentDefaultOCDB=$(setYear ${oneInputFile} ${defaultOCDB})
1552 fi
1553
1554 echo "submitting run ${runNumber} with OCDB ${currentDefaultOCDB}"
1555
1556 ###############################################################################
1557 #run one chunk with valgrind:
1558 if [[ -n ${profilingCommand} ]]; then
1559 [[ -z ${nEventsProfiling} ]] && nEventsProfiling=2
1560 [[ -z ${profilingCommand} ]] && profilingCommand="/usr/bin/valgrind --tool=callgrind --num-callers=40 -v --trace-children=yes"
1561 submit "valgrind" 1 1 000 "${alirootEnv} ${self}" CPass0 ${commonOutputPath}/000${runNumber}/valgrind ${oneInputFile} ${nEventsProfiling} ${currentDefaultOCDB} ${configFile} ${runNumber} valgrind useProfilingCommand=${profilingCommand} "${extraOpts[@]}"
1562 fi
1563
1564 ################################################################################
1565 ################################################################################
1566 # run the CPass0 if requested
1567
1568 if [ ${runCPass0reco} -eq 1 ]; then
1569
1570 echo
1571 echo "starting CPass0... for run ${runNumber}"
1572 echo
1573
1574 # create directory and copy all files that are needed
1575 targetDirectory="${commonOutputPath}/000${runNumber}/cpass0"
1576 mkdir -p ${targetDirectory}
1577
1578 filesCPass0=(
1579 "${configPath}/runCPass0.sh"
1580 "${configPath}/recCPass0.C"
1581 "${configPath}/runCalibTrain.C"
1582 "${configPath}/localOCDBaccessConfig.C"
1583 "${configPath}/OCDB*.root"
1584 "${configPath}/sim.C"
1585 "${configPath}/rec.C"
1586 "${configPath}/Config.C"
1587 )
1588 for file in ${filesCPass0[*]}; do
1589 [[ -f ${file} ]] && echo "copying ${file}" && cp -f ${file} ${commonOutputPath}
1590 done
1591
1592 localInputList=${targetDirectory}/${inputList##*/}
1593 [[ ! -f ${localInputList} ]] && egrep "\/000${runNumber}\/" ${inputList} > ${localInputList}
1594 # limit nFiles to nMaxChunks
1595 nFiles=$(wc -l < ${localInputList})
1596 [[ ${nFiles} -eq 0 ]] && echo "list contains ZERO files! exiting..." && return 1
1597 echo "raw files in list: ${nFiles}"
1598 if [[ ${nMaxChunks} -gt 0 && ${nMaxChunks} -le ${nFiles} ]]; then
1599 nFiles=${nMaxChunks}
1600 fi
1601 echo "raw files to process: ${nFiles}"
1602 [[ -z "${percentProcessedFilesToContinue}" ]] && percentProcessedFilesToContinue=100
1603 if [[ ${percentProcessedFilesToContinue} -eq 100 ]]; then
1604 nFilesToWaitFor=${nFiles}
1605 else
1606 nFilesToWaitFor=$(( ${nFiles}-${nFiles}/(100/(100-${percentProcessedFilesToContinue})) ))
1607 fi
1608 echo "requested success rate is ${percentProcessedFilesToContinue}%"
1609 echo "merging will start after ${nFilesToWaitFor} jobs are done"
1610
1611 submit ${JOBID1} 1 ${nFiles} 000 "${alirootEnv} ${self}" CPass0 ${targetDirectory} ${localInputList} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} -1 "${extraOpts[@]}"
1612
1613 ## submit a monitoring job that will run until a certain number of jobs are done with reconstruction
1614 submit "${JOBID1wait}" 1 1 000 "${alirootEnv} ${self}" WaitForOutput ${commonOutputPath} "meta/cpass0.job*.run${runNumber}.done" ${nFilesToWaitFor} ${maxSecondsToWait} '-maxdepth 1'
1615 LASTJOB=${JOBID1wait}
1616
1617 fi #end running CPass0
1618 ################################################################################
1619
1620
1621 ################################################################################
1622 # submit merging of CPass0, depends on the reconstruction
1623
1624 if [ ${runCPass0MergeMakeOCDB} -eq 1 ]; then
1625
1626 echo
1627 echo "submit CPass0 merging for run ${runNumber}"
1628 echo
1629
1630 targetDirectory="${commonOutputPath}/000${runNumber}/cpass0"
1631 mkdir -p ${targetDirectory}
1632
1633 #copy the scripts
1634 filesMergeCPass0=(
1635 "${configPath}/OCDB.root"
1636 "${configPath}/mergeMakeOCDB.byComponent.sh"
1637 "${configPath}/mergeMakeOCDB.sh"
1638 "${configPath}/localOCDBaccessConfig.C"
1639 "${configPath}/mergeByComponent.C"
1640 "${configPath}/makeOCDB.C"
1641 "${configPath}/merge.C"
1642 )
1643 for file in ${filesMergeCPass0[*]}; do
1644 [[ -f ${file} ]] && echo "copying ${file}" && cp -f ${file} ${commonOutputPath}
1645 done
1646
1647 submit ${JOBID2} 1 1 "${LASTJOB}" "${alirootEnv} ${self}" MergeCPass0 ${targetDirectory} ${currentDefaultOCDB} ${configFile} ${runNumber} cpass0.calib.run${runNumber}.list "${extraOpts[@]}"
1648 LASTJOB=${JOBID2}
1649
1650 if [[ -n ${generateMC} ]]; then
1651 submit "mrl${JOBpostfix}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" PrintValues sim ${commonOutputPath}/meta/sim.run${runNumber}.list ${commonOutputPath}/meta/cpass0.job*.run${runNumber}.done
1652 LASTJOB="mrl${JOBpostfix}"
1653 fi
1654
1655 echo
1656 fi
1657 # end of merging CPass0
1658 ################################################################################
1659
1660 ################################################################################
1661 ################################################################################
1662 # run the CPass1 if requested
1663
1664 if [ ${runCPass1reco} -eq 1 ]; then
1665
1666 targetDirectory="${commonOutputPath}/000${runNumber}/cpass1"
1667 rm -f ${commonOutputPath}/meta/cpass1.job*.run${runNumber}.done
1668
1669 # safety feature: if we are re-running for any reason we want to delete the previous output first.
1670 [[ -d ${targetDirectory} ]] && rm -rf ${targetDirectory}/* && echo "removed old output at ${targetDirectory}/*"
1671
1672 echo
1673 echo "starting CPass1... for run ${runNumber}"
1674 echo
1675
1676 # create directory and copy all files that are needed
1677 mkdir -p ${targetDirectory}
1678
1679 filesCPass1=(
1680 "${configPath}/runCPass1.sh"
1681 "${configPath}/recCPass1.C"
1682 "${configPath}/recCPass1_OuterDet.C"
1683 "${configPath}/runCalibTrain.C"
1684 "${configPath}/QAtrain_duo.C"
1685 "${configPath}/localOCDBaccessConfig.C"
1686 "${configPath}/OCDB.root"
1687 )
1688 for file in ${filesCPass1[*]}; do
1689 [[ -f ${file} ]] && echo "copying ${file}" && cp -f ${file} ${commonOutputPath}
1690 done
1691
1692 if [[ -n ${generateMC} ]]; then
1693 localInputList=${commonOutputPath}/meta/sim.run${runNumber}.list
1694 else
1695 localInputList=${targetDirectory}/${inputList##*/}
1696 [[ ! -f ${localInputList} ]] && egrep "\/000${runNumber}\/" ${inputList} > ${localInputList}
1697 fi
1698 # limit nFiles to nMaxChunks
1699 nFiles=$(wc -l < ${localInputList})
1700 [[ ${nFiles} -eq 0 ]] && echo "list contains ZERO files! continuing..." && continue
1701 echo "raw files in list: ${nFiles}"
1702 if [[ ${nMaxChunks} -gt 0 && ${nMaxChunks} -le ${nFiles} ]]; then
1703 nFiles=${nMaxChunks}
1704 fi
1705 echo "raw files to process: ${nFiles}"
1706 [[ -z "${percentProcessedFilesToContinue}" ]] && percentProcessedFilesToContinue=100
1707 if [[ ${percentProcessedFilesToContinue} -eq 100 ]]; then
1708 nFilesToWaitFor=${nFiles}
1709 else
1710 nFilesToWaitFor=$(( ${nFiles}-${nFiles}/(100/(100-${percentProcessedFilesToContinue})) ))
1711 fi
1712 echo "requested success rate is ${percentProcessedFilesToContinue}%"
1713 echo "merging will start after ${nFilesToWaitFor} jobs are done"
1714
1715 submit ${JOBID4} 1 ${nFiles} "${LASTJOB}" "${alirootEnv} ${self}" CPass1 ${targetDirectory} ${localInputList} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} -1 "${extraOpts[@]}"
1716
1717 ################################################################################
1718 ## submit a monitoring job that will run until a certain number of jobs are done with reconstruction
1719 submit "${JOBID4wait}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" WaitForOutput ${commonOutputPath} "meta/cpass1.job*.run${runNumber}.done" ${nFilesToWaitFor} ${maxSecondsToWait} '-maxdepth 1'
1720 LASTJOB=${JOBID4wait}
1721 ################################################################################
1722
1723 echo
1724 fi #end running CPass1
1725
1726 ################################################################################
1727 # submit merging of CPass1, depends on the reconstruction
1728 if [ ${runCPass1MergeMakeOCDB} -eq 1 ]; then
1729
1730 echo
1731 echo "submit CPass1 merging for run ${runNumber}"
1732 echo
1733
1734 targetDirectory="${commonOutputPath}/000${runNumber}/cpass1"
1735 rm -f ${commonOutputPath}/meta/merge.cpass1.run${runNumber}.done
1736 mkdir -p ${targetDirectory}
1737
1738 # copy files
1739 filesMergeCPass1=(
1740 "${configPath}/OCDB.root"
1741 "${configPath}/localOCDBaccessConfig.C"
1742 "${configPath}/mergeMakeOCDB.byComponent.sh"
1743 "${configPath}/mergeByComponent.C"
1744 "${configPath}/makeOCDB.C"
1745 "${configPath}/merge.C"
1746 "${configPath}/mergeMakeOCDB.sh"
1747 "${configPath}/QAtrain_duo.C"
1748 )
1749 for file in ${filesMergeCPass1[*]}; do
1750 [[ -f ${file} ]] && echo "copying ${file}" && cp -f ${file} ${commonOutputPath}
1751 done
1752
1753 submit "${JOBID5}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" MergeCPass1 ${targetDirectory} ${currentDefaultOCDB} ${configFile} ${runNumber} cpass1.calib.run${runNumber}.list cpass1.QA.run${runNumber}.lastMergingStage.txt.list cpass1.filtered.run${runNumber}.list "${extraOpts[@]}"
1754 LASTJOB=${JOBID5}
1755 echo
1756 fi
1757
1758 ###############################
1759 #if [ ${runESDfiltering} -eq 1 ]; then
1760 # rm -f ${commonOutputPath}/cpass1.ESD.run${runNumber}.list
1761 # rm -f ${commonOutputPath}/meta/filtering.cpass1.run*.done
1762 # echo
1763 # echo submitting filtering for run ${runNumber}
1764 # echo
1765 # submit "${JOBmakeESDlistCPass1}" 1 1 "${LASTJOB}" "${self}" PrintValues esd ${commonOutputPath}/meta/cpass1.ESD.run${runNumber}.list ${commonOutputPath}/meta/cpass1.job*.run${runNumber}.done
1766 # submit "${JOBfilterESDcpass1}" 1 1 "${JOBmakeESDlistCPass1}" "${alirootEnv} ${self}" MakeFilteredTrees ${commonOutputPath}/000${runNumber}/cpass1 ${runNumber} ${commonOutputPath}/meta/cpass1.ESD.run${runNumber}.list ${filteringFactorHighPt} ${filteringFactorV0s} ${currentDefaultOCDB} 1000000 0 10000000 0 ${configFile} AliESDs_Barrel.root "${extraOpts[@]}"
1767 # LASTJOB=${JOBfilterESDcpass1}
1768 #fi
1769
1770 done
1771
1772 #################################################################################
1773 #################################################################################
1774 #if [ ${runESDfiltering} -eq 1 ]; then
1775 # submit "${JOBID5wait}" 1 1 "${LASTJOB}" "${self}" WaitForOutput ${commonOutputPath} "meta/filtering.cpass1.run*.done" "${#listOfRuns[@]}" ${maxSecondsToWait}
1776 #else
1777 submit "${JOBID5wait}" 1 1 "${LASTJOB}" "${self}" WaitForOutput ${commonOutputPath} "meta/merge.cpass1.run*.done" ${#listOfRuns[@]} ${maxSecondsToWait}
1778 #fi
1779 LASTJOB=${JOBID5wait}
1780
1781 #################################################################################
1782 echo
1783 echo "submit make a summary"
1784 echo
1785
1786 submit "${JOBID6}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" MakeSummary ${configFile}
1787 LASTJOB=${JOBID6}
1788 #################################################################################
1789
1790 #restore stdout
1791 exec 1>&7 7>&-
1792 echo "jobs submitted."
1793 return 0
1794}
1795
1796goWaitForOutput()
1797{
1798 umask 0002
1799 [[ $# -lt 3 ]] && echo "goWaitForOutput() wrong number of arguments, exiting.." && return 1
1800 echo searchPath=${1}
1801 echo fileName=${2}
1802 echo numberOfFiles=${3}
1803 echo maxSecondsToWait=${4}
1804 searchPath=${1}
1805 fileName=${2}
1806 numberOfFiles=${3}
1807 maxSecondsToWait=${4}
1808 extraFindOptions=${5}
1809 echo "command to be executed: /bin/ls -1 ${searchPath}/${fileName} ${extraFindOptions}"
1810 [[ -z "${maxSecondsToWait}" ]] && maxSecondsToWait=$(( 3600*12 ))
1811 while true; do
1812 #n=$(find ${searchPath} ${extraFindOptions} -name "${fileName}" | wc -l)
1813 n=$(/bin/ls -1 ${searchPath}/${fileName} 2>/dev/null | wc -l)
1814 [[ ${n} -gt 0 ]] && echo "found ${n} X ${fileName}"
1815 [[ ${n} -ge ${numberOfFiles} ]] && break
1816 [[ ${SECONDS} -gt ${maxSecondsToWait} ]] && echo "timeout of ${maxSecondsToWait}s!" && break
1817 sleep 60
1818 done
1819 echo "DONE! exiting..."
1820 return 0
1821}
1822
1823mergeSysLogs()
1824{
1825 outputFile=${1}
1826 shift
1827 inputFiles="$@"
1828 i=0
1829 if ! ls -1 ${inputFiles} &>/dev/null; then echo "the files dont exist!: ${inputFiles}"; return 1; fi
1830 while read x; do
1831 runNumber=$(guessRunNumber ${x})
1832 [[ -z ${runNumber} ]] && echo "run number cannot be guessed for ${x}" && continue
1833 awk -v run=${runNumber} -v i=${i} 'NR > 1 {print run" "$0} NR==1 && i==0 {print "run/I:"$0}' ${x}
1834 (( i++ ))
1835 done < <(ls -1 ${inputFiles}) > ${outputFile}
1836 return 0
1837}
1838
1839goMakeMergedSummaryTree()
1840{
1841 # create list of calibration entries
1842 # takes no arguments, just run it in the base output
1843 # directory with the following files in the working directory
1844 #
1845 # Calibration file lists:
1846 # cpass0.dcsTree.list, cpass1.dcsTree.list
1847 # QA trending root file:
1848 # trending.root
1849 #
1850 # Production infoo ascii files:
1851 # summary_pass0.tree
1852 # summary_pass1.tree
1853 #
1854
1855 [[ ! -f cpass0.dcsTree.list ]] && echo "no cpass0.dcsTree.list" && return 1
1856 [[ ! -f cpass1.dcsTree.list ]] && echo "no cpass1.dcsTree.list" && return 1
1857 [[ ! -f trending.root ]] && echo "no trending.root" && return 1
1858 [[ ! -f summary_pass0.tree ]] && echo "no summary_pass0.tree" && return 1
1859 [[ ! -f summary_pass1.tree ]] && echo "no summary_pass1.tree" && return 1
1860
1861 #first, dump the C macro to file
1862 cat << EOF > mergeTree.C
1863 //
1864 // Merge summary information
1865 // Following files are expected to be in the working directory
1866 //
1867 // Calibration file lists:
1868 // cpass0.dcsTree.list, cpass1.dcsTree.list
1869 // QA trending root file:
1870 // trending.root
1871 //
1872 // Production infoo ascii files:
1873 // summary_pass0.tree
1874 // summary_pass1.tree
1875 //
1876 void mergeTree(){
1877 //
1878 //
1879 //
1880 // Calibration values dump
1881 //
1882 AliXRDPROOFtoolkit::MakeTreeFromList("Calib.TPC.CPass0.root", "dcs","dcs","cpass0.dcsTree.list",1);
1883 AliXRDPROOFtoolkit::MakeTreeFromList("Calib.TPC.CPass1.root", "dcs","dcs","cpass1.dcsTree.list",1);
1884 //
1885 // Calibration status dump
1886 //
1887 TFile *fprod = TFile::Open("fproduction.root","recreate");
1888 TTree tree0, tree1;
1889 tree0.ReadFile("summary_pass0.tree");
1890 tree1.ReadFile("summary_pass1.tree");
1891 tree0.Write("CPass0");
1892 tree1.Write("CPass1");
1893 fprod->Close();
1894 //
1895 //
1896 //
1897 TString stringSetup="";
1898 stringSetup+="1#QA.TPC#run#SummaryTPCQA/tpcQA#trending.root+"; //
1899 stringSetup+="1#Calib.TPC.CPass0#run#dcs#Calib.TPC.CPass0.root+"; //
1900 stringSetup+="1#Calib.TPC.CPass1#run#dcs#Calib.TPC.CPass1.root+"; //
1901 //
1902 stringSetup+="1#CPass0#runnumber#CPass0#fproduction.root+"; //
1903 stringSetup+="1#CPass1#runnumber#CPass1#fproduction.root+"; //
1904 //
1905 AliXRDPROOFtoolkit::JoinTreesIndex("outAll.root","joinAll","run",stringSetup.Data(), 1);
1906 }
1907EOF
1908
1909 aliroot -b -q "mergeTree.C" > mergeTrees.log
1910 return $?
1911}
1912
1913goMakeSummary()
1914{
1915 #all the final stuff goes in here for ease of use:
1916 # summary logs
1917 # qa plot making
1918 # final file lists
1919 #some defaults:
1920 log="summary.log"
1921 productionID="qa"
1922
1923 configFile=${1}
1924 shift 1
1925 extraOpts=("$@")
1926 if ! parseConfig ${configFile} "${extraOpts[@]}"; then return 1; fi
1927
1928 [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
1929
1930 exec &> >(tee ${log})
1931
1932 [[ ! -f ${configFile} ]] && echo "no config file ${configFile}!" && return
1933
1934 [[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
1935
1936 #summarize the global stuff
1937 echo "env script: ${alirootSource} ${alirootEnv}"
1938 echo "\$ALICE_ROOT=${ALICE_ROOT}"
1939 echo "commonOutputPath=${commonOutputPath}"
1940
1941 #summarize the stacktraces
1942 awk '
1943 BEGIN {
1944 print "frame/I:method/C:line/C:cpass/I:aliroot/I";
1945 RS="#[0-9]*";
1946 aliroot=0;
1947 }
1948 {
1949 if ($3 ~ /Ali*/) aliroot=1; else aliroot=0;
1950 gsub("#","",RT);
1951 if ($NF!="" && RT!="" && $3!="") print RT" "$3" "$NF" "0" "aliroot
1952 }
1953 ' 000*/cpass0/*/stacktrace* 2>/dev/null > stacktrace.tree
1954 awk '
1955 BEGIN {
1956 RS="#[0-9]*";
1957 aliroot=0;
1958 }
1959 {
1960 if ($3 ~ /Ali*/) aliroot=1; else aliroot=0;
1961 gsub("#","",RT);
1962 if ($NF!="" && RT!="" && $3!="") print RT" "$3" "$NF" "1" "aliroot
1963 }
1964 ' 000*/cpass1/*/stacktrace* 2>/dev/null >> stacktrace.tree
1965
1966 echo total numbers for the production:
1967 echo
1968 awk 'BEGIN {nFiles=0;nCore=0;}
1969 /^calibfile/ {nFiles++;}
1970 /core dumped/ {nCore++i;}
1971 END {print "cpass0 produced "nFiles" calib files, "nCore" core files";}' meta/cpass0.job*done 2>/dev/null
1972 awk 'BEGIN {nOK=0; nBAD=0; }
1973 /\/rec.log OK/ {nOK++;}
1974 /\/rec.log BAD/ {nBAD++;}
1975 /stderr BAD/ {if ($0 ~ /rec.log/){nBAD++;}}
1976 END {print "cpass0 reco: OK: "nOK"\tBAD: "nBAD;}' meta/cpass0.job*done 2>/dev/null
1977 awk 'BEGIN {nOK=0; nBAD=0; }
1978 /\/calib.log OK/ {nOK++;}
1979 /\/calib.log BAD/ {nBAD++;}
1980 END {print "cpass0 calib: OK: "nOK"\tBAD: "nBAD;}' meta/cpass0.job*done 2>/dev/null
1981
1982 awk 'BEGIN {nOK=0; nBAD=0; }
1983 /merge.log OK/ {nOK++;}
1984 /merge.log BAD/ {nBAD++;}
1985 END {print "cpass0 merge: OK: "nOK"\tBAD: "nBAD;}' meta/merge.cpass0*done 2>/dev/null
1986 awk 'BEGIN {nOK=0; nBAD=0; }
1987 /ocdb.log OK/ {nOK++;}
1988 /ocdb.log BAD/ {nBAD++;}
1989 END {print "cpass0 OCDB: OK: "nOK"\tBAD: "nBAD;}' meta/merge.cpass0*done 2>/dev/null
1990
1991 echo
1992 awk 'BEGIN {nFiles=0;nCore=0;}
1993 /^calibfile/ {nFiles++;}
1994 /core dumped/ {nCore++;}
1995 END {print "cpass1 produced "nFiles" calib files, "nCore" core files";}' meta/cpass1.job*done 2>/dev/null
1996 awk 'BEGIN {nOK=0; nBAD=0; }
1997 /\/rec.log OK/ {nOK++;}
1998 /\/rec.log BAD/ {nBAD++;}
1999 /stderr BAD/ {if ($0 ~ /rec.log/){nBAD++;}}
2000 END {print "cpass1 reco: OK: "nOK"\tBAD: "nBAD;}' meta/cpass1.job*done 2>/dev/null
2001 awk 'BEGIN {nOK=0; nBAD=0; }
2002 /\/calib.log OK/ {nOK++;}
2003 /\/calib.log BAD/ {nBAD++;}
2004 END {print "cpass1 calib: OK: "nOK"\tBAD: "nBAD;}' meta/cpass1.job*done 2>/dev/null
2005
2006 awk 'BEGIN {nOK=0; nBAD=0; }
2007 /merge.log OK/ {nOK++;}
2008 /merge.log BAD/ {nBAD++;}
2009 END {print "cpass1 merge: OK: "nOK"\tBAD: "nBAD;}' meta/merge.cpass1*done 2>/dev/null
2010 awk 'BEGIN {nOK=0; nBAD=0; }
2011 /ocdb.log OK/ {nOK++;}
2012 /ocdb.log BAD/ {nBAD++;}
2013 END {print "cpass1 OCDB: OK: "nOK"\tBAD: "nBAD;}' meta/merge.cpass1*done 2>/dev/null
2014
2015 echo
2016 echo per run stats:
2017 /bin/ls -1 meta/merge.cpass0.run*.done | while read x
2018do
2019 dir=$(goPrintValues calibfile - ${x})
2020 runNumber=$(guessRunNumber ${dir})
2021 [[ -z ${runNumber} ]] && continue
2022
2023 if $(/bin/ls meta/cpass0.job*.run${runNumber}.done &> /dev/null); then
2024 statusCPass0=( $(
2025 awk 'BEGIN {nOKrec=0;nBADrec=0;nOKcalib=0;nBADcalib=0;nOKstderr=0;nBADstderr=0;}
2026 /\/rec.log OK/ {nOKrec++;}
2027 /\/rec.log BAD/ {nBADrec++;}
2028 /stderr BAD/ {if ($0 ~ /rec.log/) {nBADrec++;} nBADstderr++;}
2029 /stderr OK/ {nOKstderr++;}
2030 /\/calib.log OK/ {nOKcalib++;}
2031 /\/calib.log BAD/ {nBADcalib++}
2032 END {print ""nOKrec" "nBADrec" "nOKstderr" "nBADstderr" "nOKcalib" "nBADcalib;}' meta/cpass0.job*.run${runNumber}.done 2>/dev/null
2033 ) )
2034 fi
2035
2036 if $(/bin/ls meta/cpass1.job*.run${runNumber}.done &>/dev/null); then
2037 statusCPass1=( $(
2038 awk 'BEGIN {nOKrec=0;nBADrec=0;nOKcalib=0;nBADcalib=0;nOKstderr=0;nBADstderr=0;nQAbarrelOK=0;nQAbarrelBAD=0;nQAouterOK=0;nQAouterBAD=0;}
2039 /\/rec.log OK/ {nOKrec++;}
2040 /\/rec.log BAD/ {nBADrec++;}
2041 /stderr BAD/ {if ($0 ~ /rec.log/) nBADrec++;nBADstderr++;}
2042 /stderr OK/ {nOKstderr++;}
2043 /\/calib.log OK/ {nOKcalib++;}
2044 /\/calib.log BAD/ {nBADcalib++}
2045 /\/qa_barrel.log OK/ {nQAbarrelOK++;}
2046 /\/qa_barrel.log BAD/ {nQAbarrelBAD++;}
2047 /\/qa_outer.log OK/ {nQAouterOK++;}
2048 /\/qa_outer.log BAD/ {nQAouterBAD++;}
2049 END {print ""nOKrec" "nBADrec" "nOKstderr" "nBADstderr" "nOKcalib" "nBADcalib" "nQAbarrelOK" "nQAbarrelBAD" "nQAouterOK" "nQAouterBAD;}' meta/cpass1.job*.run${runNumber}.done 2>/dev/null
2050 ) )
2051 fi
2052
2053 statusOCDBcpass0=$(awk '/ocdb.log/ {print $2} ' ${x} 2>/dev/null)
2054 statusOCDBcpass1=$(awk '/ocdb.log/ {print $2}' ${x/cpass0/cpass1} 2>/dev/null)
2055 statusQA=$(awk '/mergeMakeOCDB.log/ {print $2}' ${x/cpass0/cpass1} 2>/dev/null)
2056
2057 printf "%s\t ocdb.log cpass0: %s\t ocdb.log cpass1: %s\tqa.log:%s\t| cpass0: rec:%s/%s stderr:%s/%s calib:%s/%s cpass1: rec:%s/%s stderr:%s/%s calib:%s/%s QAbarrel:%s/%s QAouter:%s/%s\n" ${runNumber} ${statusOCDBcpass0} ${statusOCDBcpass1} ${statusQA} ${statusCPass0[0]} ${statusCPass0[1]} ${statusCPass0[2]} ${statusCPass0[3]} ${statusCPass0[4]} ${statusCPass0[5]} ${statusCPass1[0]} ${statusCPass1[1]} ${statusCPass1[2]} ${statusCPass1[3]} ${statusCPass1[4]} ${statusCPass1[5]} ${statusCPass1[6]} ${statusCPass1[7]} ${statusCPass1[8]} ${statusCPass1[9]}
2058done
2059
2060 #make lists with output files - QA, trending, filtering and calibration
2061 ### wait for the merging of all runs to be over ###
2062 rm -f qa.list
2063 goPrintValues qafile qa.list ${commonOutputPath}/meta/merge.cpass1.run*.done &>/dev/null
2064 rm -f calib.list
2065 goPrintValues calibfile calib.list ${commonOutputPath}/meta/merge.cpass1.run*.done &>/dev/null
2066 rm -f trending.list
2067 goPrintValues trendingfile trending.list ${commonOutputPath}/meta/merge.cpass1.run*.done &>/dev/null
2068 rm -f filtering.list
2069 goPrintValues filteredTree filtering.list ${commonOutputPath}/meta/merge.cpass1.run*.done &>/dev/null
2070 #/bin/ls ${commonOutputPath}/*/cpass0/dcs* > cpass0.dcsTree.list
2071 rm -f cpass0.dcsTree.list
2072 goPrintValues dcsTree cpass0.dcsTree.list ${commonOutputPath}/meta/merge.cpass0.run*.done &>/dev/null
2073 #/bin/ls ${commonOutputPath}/*/cpass1/dcs* > cpass1.dcsTree.list
2074 rm -f cpass1.dcsTree.list
2075 goPrintValues dcsTree cpass1.dcsTree.list ${commonOutputPath}/meta/merge.cpass1.run*.done &>/dev/null
2076
2077 #merge trending
2078 rm -f ${commonOutputPath}/trending_merged.root
2079 goMerge trending.list ${commonOutputPath}/trending.root ${configFile} "${extraOpts[@]}" &> mergeTrending.log
2080
2081 goMakeSummaryTree ${commonOutputPath} 0
2082 goMakeSummaryTree ${commonOutputPath} 1
2083
2084 goCreateQAplots "qa.list" "${productionID}" "QAplots" "${configFile}" "${extraOpts[@]}" filteringList="filtering.list" &>createQAplots.log
2085
2086 #make a merged summary tree out of the QA trending, dcs trees and log summary trees
2087 goMakeMergedSummaryTree
2088
2089 #if set, email the summary
2090 [[ -n ${MAILTO} ]] && cat ${log} | mail -s "benchmark ${productionID} done" ${MAILTO}
2091
2092 return 0
2093}
2094
2095goMakeSummaryTree()
2096{
2097 if [[ $# -lt 1 ]] ; then
2098 return
2099 fi
2100 #1. define vars/arrays
2101 DIR=${1} #use input or exec in current dir
2102 pass=${2-"0"} #pass from input
2103 outfile="summary_pass${pass}.tree"
2104 Ncolumns=0
2105 test -f ${outfile} && : >${outfile}
2106 errfile=${outfile/tree/err}
2107 test -f ${errfile} && : >${errfile}
2108
2109 declare -a counterString=(TOFevents TOFtracks TPCevents TPCtracks TRDevents TRDtracks T0events SDDevents SDDtracks MeanVertexevents)
2110 Ncounter=${#counterString[@]}
2111
2112 declare -a statusString=(TRDStatus TOFStatus TPCStatus T0Status MeanVertexStatus)
2113 Nstatus=${#statusString[@]}
2114
2115
2116 declare -a ratesString=(rec stderr calib qa_barrel qa_outer)
2117 Nrates=${#ratesString[@]}
2118
2119 runs=( $(ls -1 ${DIR}/meta/merge.cpass0* | while read x; do guessRunNumber $x; done) )
2120 Nruns=${#runs[@]}
2121
2122 echo -n runnumber/I >>${outfile}
2123 echo -n :cpass${pass}status/I >>${outfile}
2124 echo -n :cpass${pass}QAstatus/I >>${outfile}
2125 for i in ${ratesString[@]}; do
2126 echo -n :${i}OK/I >>${outfile}
2127 echo -n :${i}BAD/I >>${outfile}
2128
2129 done
2130 for i in ${counterString[@]} ${statusString[@]} ; do
2131 echo -n :${i}/I >>${outfile}
2132 done
2133 Ncolumns=$((2 + 2*Nrates + Ncounter + Nstatus))
2134 echo >> ${outfile}
2135
2136 #2. loop runs
2137
2138 for runnumber in ${runs[@]} ; do
2139
2140
2141
2142 filejob="${DIR}/meta/cpass${pass}.job*.run${runnumber}.done"
2143 filemerge="${DIR}/meta/merge.cpass${pass}.run${runnumber}.done"
2144 fileOCDB=$(grep /ocdb.log ${filemerge} | awk '{print $1}')
2145 if ! $(/bin/ls ${filemerge} &>/dev/null) ; then
2146 echo "${filemerge} does not exist!" >>${errfile}
2147 continue
2148 elif ! $(/bin/ls ${filejob} &>/dev/null) ; then
2149 echo "${filejob} does not exist!" >>${errfile}
2150 echo -n ${runnumber} >> ${outfile}
2151 for i in $(seq ${Ncolumns}) ; do
2152 echo -n "-1" >> ${outfile}
2153 done
2154 echo >> ${outfile}
2155 continue
2156 fi
2157 echo -n ${runnumber} >> ${outfile}
2158 #pass0status= grep '/ocdb.log' ${filemerge} | cut -d' ' -f2 | tr OK x1 | tr BAD xx0 | tr -d 'x'
2159 passStatus=$(grep '/ocdb.log' ${filemerge} | grep OK | wc -l)
2160 echo -n " ${passStatus}" >> ${outfile}
2161 qaStatus=$(grep '/mergeMakeOCDB.log' ${filemerge} | grep OK | wc -l)
2162 echo -n " ${qaStatus}" >> ${outfile}
2163
2164
2165 #fill OK/BAD rates
2166 for i in $(seq 0 $((${Nrates}-1))) ; do
2167 var1=$(grep "/${ratesString[${i}]}.log" ${filejob} | grep OK | wc -l)
2168 var2=$(grep "/${ratesString[${i}]}.log" ${filejob} | grep BAD | wc -l)
2169
2170 if [[ ${ratesString[${i}]} == "stderr" ]] ; then
2171 var1=$(grep "stderr" ${filejob} | grep OK | wc -l)
2172 var2=$(grep "stderr" ${filejob} | grep "rec.log" | grep BAD | wc -l)
2173 fi
2174 echo -n " ${var1}" >> ${outfile}
2175 echo -n " ${var2}" >> ${outfile}
2176 done
2177
2178 if [[ -f ${fileOCDB} ]] ; then
2179 #fill counter
2180 for i in $(seq 0 $((${Ncounter}-1))) ; do
2181 var1=$(grep Monalisa ${fileOCDB} | grep ${counterString[${i}]} | cut -f2)
2182 echo -n " ${var1:-"-1"}" >> ${outfile}
2183 done
2184
2185 #fill status
2186 for i in $(seq 0 $((${Nstatus}-1))) ; do
2187 var1=$(grep "calibration status=" ${fileOCDB} | grep ${statusString[${i}]/Status/} | cut -d'=' -f2)
2188 echo -n " ${var1:-"-1"}" >> ${outfile}
2189 done
2190 fi
2191 echo >> ${outfile}
2192 done
2193
2194 return 0
2195}
2196
2197parseConfig()
2198{
2199 configFile=${1}
2200 shift
2201 args=("$@")
2202
2203 #some defaults
2204 #autoOCDB=0
2205 defaultOCDB="raw://"
2206 #runNumber=167123
2207 #makeflowPath="/hera/alice/aux/cctools/bin"
2208 #makeflowOptions="-T wq -N alice -d all -C ali-copilot.cern.ch:9097"
2209 #makeflowOptions="-T wq -N alice -C ali-copilot.cern.ch:9097"
2210 makeflowOptions=""
2211 batchCommand="/usr/bin/qsub"
2212 batchFlags="-b y -cwd -l h_rt=24:0:0,h_rss=4G "
2213 baseOutputDirectory="$PWD/output"
2214 #alirootEnv="/cvmfs/alice.cern.ch/bin/alienv setenv AliRoot/v5-04-34-AN -c"
2215 #alirootEnv="/home/mkrzewic/alisoft/balice_master.sh"
2216 #trustedQAtrainMacro='/hera/alice/mkrzewic/gsisvn/Calibration/QAtrain_duo.C'
2217 reconstructInTemporaryDir=0
2218 recoTriggerOptions="\"\""
2219 percentProcessedFilesToContinue=100
2220 maxSecondsToWait=$(( 3600*24 ))
2221 nEvents=-1
2222 nMaxChunks=0
2223 postSetUpActionCPass0=""
2224 postSetUpActionCPass1=""
2225 runCPass0reco=1
2226 runCPass0MergeMakeOCDB=1
2227 runCPass1reco=1
2228 runCPass1MergeMakeOCDB=1
2229 runESDfiltering=1
2230 filteringFactorHighPt=1e2
2231 filteringFactorV0s=1e1
2232 MAILTO=""
2233 #pretend=1
2234 #dontRedirectStdOutToLog=1
2235 logToFinalDestination=1
2236 ALIROOT_FORCE_COREDUMP=1
2237
2238 #first, source the config file
2239 if [ -f ${configFile} ]; then
2240 source ${configFile}
2241 else
2242 echo "config file ${configFile} not found!, skipping..."
2243 fi
2244
2245 #then, parse the options as they override the options from file
2246 for opt in "${args[@]}"; do
2247 if [[ ! "${opt}" =~ .*=.* ]]; then
2248 echo "badly formatted option ${var}, should be: option=value, stopping..."
2249 return 1
2250 fi
2251 local var="${opt%%=*}"
2252 local value="${opt#*=}"
2253 echo "${var} = ${value}"
2254 export ${var}="${value}"
2255 done
2256
2257 #do some checking
2258 [[ -z ${alirootEnv} ]] && echo "alirootEnv not defined!" && return 1
2259
2260 #export the aliroot function if defined to override normal behaviour
2261 [[ $(type -t aliroot) =~ "function" ]] && export -f aliroot
2262
2263 return 0
2264}
2265
2266aliroot()
2267{
2268 args="$@"
2269 if [[ -n ${useProfilingCommand} ]]; then
2270 valgrindLogFile="cpu.txt"
2271 [[ "${args}" =~ rec ]] && valgrindLogFile="cpu_rec.txt"
2272 [[ "${args}}" =~ Calib ]] && valgrindLogFile="cpu_calib.txt"
2273 [[ -n ${useProfilingCommand} ]] && useProfilingCommand="${useProfilingCommand} --log-file=${valgrindLogFile}"
2274 echo running ${useProfilingCommand} aliroot ${args}
2275 ${useProfilingCommand} aliroot ${args}
2276 else
2277 #to prevent an infinite recursion use "command aliroot" to disable
2278 #aliases and functions
2279 echo running command aliroot ${args}
2280 command aliroot "$@"
2281 fi
2282 return 0
2283}
2284
2285guessRunData()
2286{
2287 #guess the period from the path, pick the rightmost one
2288 period=""
2289 runNumber=""
2290 year=""
2291 pass=""
2292 legoTrainRunNumber=""
2293 dataType=""
2294
2295 local shortRunNumber=""
2296 local IFS="/"
2297 declare -a path=( $1 )
2298 local dirDepth=$(( ${#path[*]}-1 ))
2299 i=0
2300 #for ((x=${dirDepth};x>=0;x--)); do
2301 for ((x=0;x<=${dirDepth};x++)); do
2302
2303 [[ $((x-1)) -ge 0 ]] && local fieldPrev=${path[$((x-1))]}
2304 local field=${path[${x}]}
2305 local fieldNext=${path[$((x+1))]}
2306
2307 [[ ${field} =~ ^[0-9]*$ && ${fieldNext} =~ (.*\.zip$|.*\.root$) ]] && legoTrainRunNumber=${field}
2308 [[ -n ${legoTrainRunNumber} && -z ${pass} ]] && pass=${fieldPrev}
2309 [[ ${field} =~ ^LHC[0-9][0-9][a-z].*$ ]] && period=${field%_*}
2310 [[ ${field} =~ ^000[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && runNumber=${field#000}
2311 [[ ${field} =~ ^[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && shortRunNumber=${field}
2312 [[ ${field} =~ ^20[0-9][0-9]$ ]] && year=${field}
2313 [[ ${field} =~ ^(^sim$|^data$) ]] && dataType=${field}
2314 (( i++ ))
2315 done
2316 [[ -z ${legoTrainRunNumber} ]] && pass=${path[$((dirDepth-1))]}
2317 [[ "${dataType}" =~ ^sim$ ]] && pass="passMC" && runNumber=${shortRunNumber}
2318
2319 #if [[ -z ${dataType} || -z ${year} || -z ${period} || -z ${runNumber}} || -z ${pass} ]];
2320 if [[ -z ${runNumber}} ]];
2321 then
2322 #error condition
2323 return 1
2324 else
2325 #ALL OK
2326 return 0
2327 fi
2328 return 0
2329}
2330
2331main "$@"