echo "uses a batch system (SGE):"
echo " ${0} \"submit\" productionID inputList configFile [extraOpts]"
echo "extraOpts if non-empty override the config file, e.g.:"
- echo " ${0} submit benchmark.list test1 benchmark.config runNumber=169123 nEvents=10"
+ echo " ${0} submit test1 benchmark.list benchmark.config runNumber=169123 nEvents=10"
fi
return
fi
"WaitForOutput") goWaitForOutput "$@";;
"Merge") goMerge "$@";;
*)
- eval ${runMode} $@
+ ${runMode} "$@"
;;
esac
+ return 0
}
generateMC()
OCDBpath=${2}
nEventsim=${3}
if [[ -n ${pretend} ]]; then
+ sleep ${pretendDelay}
touch galice.root
else
if [[ -f sim.C && -f Config.C ]] ; then
}
goCPass0()
-{
+(
umask 0002
targetDirectory=${1}
runNumber=${6}
jobindex=${7}
shift 7
- parseConfig ${configFile} $@
+ if ! parseConfig ${configFile} "$@"; then return 1; fi
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
#use the jobindex only if set and non-negative
if [[ -z ${jobindex} || ${jobindex} -lt 0 ]]; then
#runpath=${PWD}/rundir_cpass0_${runNumber}_${jobindex}
runpath=${outputDir}
- [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
- [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
+ #[[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
+ [[ ${reconstructInTemporaryDir} -eq 1 ]] && runpath=$(mktemp -d -t cpass0.XXXXXX)
mkdir -p ${runpath}
[[ ! -d ${runpath} ]] && echo "cannot make runpath ${runpath}" && touch ${doneFile} && return 1
- cd ${runpath}
+ if ! cd ${runpath}; then
+ echo "PWD=$PWD is not the runpath=${runpath}"
+ touch ${doneFile}
+ return 1
+ fi
#runCPassX/C expects the raw chunk to be linked in the run dir
#despite it being accessed by the full path
olddir=${PWD}
outputDirMC=${commonOutputPath}/000${runNumber}/sim/${jobindex}
simrunpath=${outputDirMC}
- [[ ${simulateInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && simrunpath=${TMPDIR}
- [[ ${simulateInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && simrunpath=$(mktemp -d)
+ #[[ ${simulateInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && simrunpath=${TMPDIR}
+ [[ ${simulateInTemporaryDir} -eq 1 ]] && simrunpath=$(mktemp -d -t cpass0MC.XXXXXX)
mkdir -p ${outputDirMC}
mkdir -p ${simrunpath}
- cd ${simrunpath}
-
- filesMC=(
- "${commonOutputPath}/sim.C"
- "${commonOutputPath}/rec.C"
- "${commonOutputPath}/Config.C"
- "${commonOutputPath}/OCDB_*.root"
- )
- for file in ${filesMC[*]}; do
- [[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
- done
+ if cd ${simrunpath}; then
- generateMC ${runNumber} ${ocdbPath} ${nEvents}
+ filesMC=(
+ "${batchWorkingDirectory}/sim.C"
+ "${batchWorkingDirectory}/rec.C"
+ "${batchWorkingDirectory}/Config.C"
+ "${batchWorkingDirectory}/OCDB_*.root"
+ )
+ for file in ${filesMC[*]}; do
+ [[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
+ done
- [[ ! "${simrunpath}" =~ "${outputDirMC}" ]] && mv * ${outputDirMC} #TODO check if it works
- cd ${olddir}
-
- ln -s ${outputDirMC}/* ${runpath}/
-
- inputList=${outputDirMC}/galice.root #TODO not valid outside shell !!!
- infile=""
+ generateMC ${runNumber} ${ocdbPath} ${nEvents}
+
+ [[ ! "${simrunpath}" =~ "${outputDirMC}" ]] && mv * ${outputDirMC} #TODO check if it works
+ cd ${olddir}
+
+ ln -s ${outputDirMC}/* ${runpath}/
+
+ inputList=${outputDirMC}/galice.root #TODO not valid outside shell !!!
+ infile=""
+ fi
fi
######
logOutputDir=${runpath}
[[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
- [[ -z ${dontRedirectStdOutToLog} ]] && exec 1> ${logOutputDir}/stdout
- [[ -z ${dontRedirectStdOutToLog} ]] && exec 2> ${logOutputDir}/stderr
+ [[ -z ${dontRedirectStdOutToLog} ]] && exec &> ${logOutputDir}/stdout
+ #[[ -z ${dontRedirectStdOutToLog} ]] && exec 2> ${logOutputDir}/stderr
echo "${0} $*"
echo "#####################"
alirootInfo > ALICE_ROOT.log
filesCPass0=(
- "${commonOutputPath}/runCPass0.sh"
- "${commonOutputPath}/recCPass0.C"
- "${commonOutputPath}/runCalibTrain.C"
- "${commonOutputPath}/localOCDBaccessConfig.C"
- "${commonOutputPath}/OCDB.root"
+ "${batchWorkingDirectory}/runCPass0.sh"
+ "${batchWorkingDirectory}/recCPass0.C"
+ "${batchWorkingDirectory}/runCalibTrain.C"
+ "${batchWorkingDirectory}/localOCDBaccessConfig.C"
+ "${batchWorkingDirectory}/OCDB.root"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/runCPass0.sh"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/recCPass0.C"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/runCalibTrain.C"
for file in ${filesCPass0[*]}; do
[[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
+ [[ ${file##*/} =~ .*\.sh ]] && chmod +x ${file##*/}
done
echo "this directory (${PWD}) contents:"
#run CPass0
echo "${runpath}/runCPass0.sh ${infile} ${nEvents} ${runNumber} ${ocdbPath} ${recoTriggerOptions}"
if [[ -n ${pretend} ]]; then
+ sleep ${pretendDelay}
touch AliESDs.root
touch AliESDfriends.root
touch AliESDfriends_v1.root
echo rm -f ./${chunkName}
rm -f ./${chunkName}
- echo "cp --recursive ${runpath}/* ${outputDir}"
- cp -p --recursive ${runpath}/* ${outputDir}
+ echo "cp -R ${runpath}/* ${outputDir}"
+ cp -p -R ${runpath}/* ${outputDir}
echo
#validate CPass0
cd ${outputDir}
touch ${doneFile}
- [[ -f ${outputDirMC}/galice.root ]] && echo "sim ${outputDirMC}/galice.root" >> ${doneFile}
- [[ -f AliESDfriends_v1.root ]] && echo "calibfile ${outputDir}/AliESDfriends_v1.root" >> ${doneFile}
- [[ -f AliESDs.root ]] && echo "esd ${outputDir}/AliESDs.root" >> ${doneFile}
echo "dir ${outputDir}" >> ${doneFile}
- summarizeLogs >> ${doneFile}
+ if summarizeLogs >> ${doneFile}; then
+ [[ -f ${outputDirMC}/galice.root ]] && echo "sim ${outputDirMC}/galice.root" >> ${doneFile}
+ [[ -f AliESDfriends_v1.root ]] && echo "calibfile ${outputDir}/AliESDfriends_v1.root" >> ${doneFile}
+ [[ -f AliESDs.root ]] && echo "esd ${outputDir}/AliESDs.root" >> ${doneFile}
+ fi
- [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
+ [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath} && echo "removing ${runpath}"
return 0
-}
+)
goCPass1()
-{
+(
umask 0002
targetDirectory=${1}
runNumber=${6}
jobindex=${7}
shift 7
- parseConfig ${configFile} $@
+ extraOpts=("$@")
+ if ! parseConfig ${configFile} "$@"; then return 1; fi
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
#use the jobindex only if set and non-negative
if [[ -z ${jobindex} || ${jobindex} -lt 0 ]]; then
#runpath=${PWD}/rundir_cpass1_${runNumber}_${jobindex}
runpath=${outputDir}
- [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
- [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
+ #[[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
+ [[ ${reconstructInTemporaryDir} -eq 1 ]] && runpath=$(mktemp -d -t cpass1.XXXXXX)
#MC
if [[ "${infile}" =~ galice\.root ]]; then
#init the running path
mkdir -p ${runpath}
[[ ! -d ${runpath} ]] && echo "cannot make runpath ${runpath}" && touch ${doneFile} && return 1
- cd ${runpath}
+ if ! cd ${runpath}; then
+ echo "PWD=$PWD is not the runpath=${runpath}"
+ touch ${doneFile}
+ return 1
+ fi
#this is needed for runCPass1.sh
ln -s ${infile} ${runpath}/${chunkName}
logOutputDir=${runpath}
[[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
- [[ -z ${dontRedirectStdOutToLog} ]] && exec 1> ${logOutputDir}/stdout
- [[ -z ${dontRedirectStdOutToLog} ]] && exec 2> ${logOutputDir}/stderr
+ [[ -z ${dontRedirectStdOutToLog} ]] && exec &> ${logOutputDir}/stdout
+ #[[ -z ${dontRedirectStdOutToLog} ]] && exec 2> ${logOutputDir}/stderr
echo "${0} $*"
echo "#####################"
echo doneFile ${doneFile}
echo runpath ${runpath}
echo outputDir ${outputDir}
+ echo batchWorkingDirectory ${batchWorkingDirectory}
echo ALICE_ROOT ${ALICE_ROOT}
echo PWD ${PWD}
echo "########## ###########"
alirootInfo > ALICE_ROOT.log
filesCPass1=(
- "${commonOutputPath}/runCPass1.sh"
- "${commonOutputPath}/recCPass1.C"
- "${commonOutputPath}/recCPass1_OuterDet.C"
- "${commonOutputPath}/runCalibTrain.C"
- "${commonOutputPath}/QAtrain_duo.C"
- "${commonOutputPath}/localOCDBaccessConfig.C"
+ "${batchWorkingDirectory}/runCPass1.sh"
+ "${batchWorkingDirectory}/recCPass1.C"
+ "${batchWorkingDirectory}/recCPass1_OuterDet.C"
+ "${batchWorkingDirectory}/runCalibTrain.C"
+ "${batchWorkingDirectory}/QAtrain_duo.C"
+ "${batchWorkingDirectory}/localOCDBaccessConfig.C"
+ "${batchWorkingDirectory}/${configFile}"
"${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz"
- "${commonOutputPath}/OCDB.root"
+ "${batchWorkingDirectory}/OCDB.root"
"${trustedQAtrainMacro}"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/runCPass1.sh"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/recCPass1.C"
"${ALICE_ROOT}/ANALYSIS/macros/QAtrain_duo.C"
)
- for file in ${filesCPass1[*]}; do
+ for file in "${filesCPass1[@]}"; do
[[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
+ [[ ${file##*/} =~ .*\.sh ]] && echo "making ${file##*/} executable" && chmod +x ${file##*/}
done
echo "this directory (${PWD}) contents:"
/bin/ls
echo
+ #remove spaces around commas from calls to root
sed -i '/.*root .*\.C/ s|\s*,\s*|,|g' *.sh
if [[ -n ${postSetUpActionCPass1} ]]; then
#create the Barrel and OuterDet directories for CPass1 and link the local OCDB directory
#there to make the localOCDBaccessConfig.C file work, since it may point to the OCDB
#entries using a relative path, e.g. local://./OCDB
+ echo "linking the OCDB/ for Barrel and OuterDet directories"
mkdir Barrel OuterDet
+ ls -l
ln -s ../OCDB Barrel/OCDB
ln -s ../OCDB OuterDet/OCDB
+ #setup the filtering
+ #the following option enables the filtering task inside the QAtrain_duo.C
+ [[ -n $runESDfiltering ]] && export QA_TaskFilteredTree=1
+ #set the downscaling factors during the filtering fro expert QA (overrides the previous values)
+ if [[ -n ${filteringFactorHighPt} ]]; then
+ export AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF=${filteringFactorHighPt}
+ fi
+ if [[ -n ${filteringFactorV0s} ]]; then
+ export AliAnalysisTaskFilteredTree_fLowPtV0DownscaligF=${filteringFactorV0s}
+ fi
+
#run CPass1
chmod u+x runCPass1.sh
echo "${runpath}/runCPass1.sh ${infile} ${nEvents} ${runNumber} ${ocdbPath} ${recoTriggerOptions}"
if [[ -n ${pretend} ]]; then
+ sleep ${pretendDelay}
touch AliESDs_Barrel.root
touch AliESDfriends_Barrel.root
touch AliESDfriends_v1.root
touch rec.log
touch calib.log
touch qa.log
+ touch filtering.log FilterEvents_Trees.root
else
./runCPass1.sh "${infile}" "${nEvents}" "${runNumber}" "${ocdbPath}" "${recoTriggerOptions}"
+
+ [[ ! -f AliESDs_Barrel.root && -f Barrel/AliESDs.root ]] && mv Barrel/AliESDs.root AliESDs_Barrel.root
+ [[ ! -f AliESDfriends_Barrel.root && -f Barrel/AliESDfriends.root ]] && mv Barrel/AliESDfriends.root AliESDfriends_Barrel.root
+ [[ ! -f AliESDfriends_v1.root && -f Barrel/AliESDfriends_v1.root ]] && mv Barrel/AliESDfriends_v1.root .
+ [[ ! -f QAresults_barrel.root && -f Barrel/QAresults_barrel.root ]] && mv Barrel/QAresults_barrel.root .
+ [[ ! -f AliESDs_Outer.root && -f OuterDet/AliESDs.root ]] && mv OuterDet/AliESDs.root AliESDs_Outer.root
+ [[ ! -f AliESDfriends_Outer.root && -f OuterDet/AliESDfriends.root ]] && mv OuterDet/AliESDfriends.root AliESDfriends_Outer.root
+ [[ ! -f QAresults_outer.root && -f OuterDet/QAresults_outer.root ]] && mv OuterDet/QAresults_outer.root .
+ [[ ! -f FilterEvents_Trees.root && -f Barrel/FilterEvents_Trees.root ]] && mv Barrel/FilterEvents_Trees.root .
+
+ #make the filtered tree (if requested and not already produced by QA
+ [[ -f AliESDs_Barrel.root ]] && echo "AliESDs_Barrel.root" > filtered.list
+ if [[ -n ${runESDfiltering} && ! -f FilterEvents_Trees.root && -f filtered.list ]]; then
+ goMakeFilteredTrees ${PWD} ${runNumber} "${PWD}/filtered.list" ${filteringFactorHighPt} ${filteringFactorV0s} ${ocdbPath} 1000000 0 10000000 0 ${configFile} AliESDs_Barrel.root "${extraOpts[@]}" >filtering.log
+ else
+ echo ""
+ fi
+
fi
##handle possible crashes in QA (happens often in trunk)
# time aliroot -b -q "QAtrain_duo.C(\"_barrel\",${runNumber},\"wn.xml\",0,\"${ocdbPath}\")" &> ../qa_barrel_trusted.log
# cd ../
#fi
- [[ ! -f AliESDs_Barrel.root && -f Barrel/AliESDs.root ]] && mv Barrel/AliESDs.root AliESDs_Barrel.root
- [[ ! -f AliESDfriends_Barrel.root && -f Barrel/AliESDfriends.root ]] && mv Barrel/AliESDfriends.root AliESDfriends_Barrel.root
- [[ ! -f AliESDfriends_v1.root && -f Barrel/AliESDfriends_v1.root ]] && mv Barrel/AliESDfriends_v1.root .
- [[ ! -f QAresults_barrel.root && -f Barrel/QAresults_barrel.root ]] && mv Barrel/QAresults_barrel.root .
- [[ ! -f AliESDs_Outer.root && -f OuterDet/AliESDs.root ]] && mv OuterDet/AliESDs.root AliESDs_Outer.root
- [[ ! -f AliESDfriends_Outer.root && -f OuterDet/AliESDfriends.root ]] && mv OuterDet/AliESDfriends.root AliESDfriends_Outer.root
- [[ ! -f QAresults_outer.root && -f OuterDet/QAresults_outer.root ]] && mv OuterDet/QAresults_outer.root .
#move stuff to final destination
echo "this directory (${PWD}) contents:"
/bin/ls
echo rm -f ./${chunkName}
rm -f ./${chunkName}
- echo "cp --recursive ${runpath}/* ${outputDir}"
- cp -pf --recursive ${runpath}/* ${outputDir}
+ echo "cp -R ${runpath}/* ${outputDir}"
+ cp -pf -R ${runpath}/* ${outputDir}
echo
#validate CPass1
cd ${outputDir}
touch ${doneFile}
- [[ -f AliESDs_Barrel.root ]] && echo "esd ${outputDir}/AliESDs_Barrel.root" >> ${doneFile}
- [[ -f AliESDfriends_v1.root ]] && echo "calibfile ${outputDir}/AliESDfriends_v1.root" >> ${doneFile}
- [[ -f QAresults_Barrel.root ]] && echo "qafile ${outputDir}/QAresults_Barrel.root" >> ${doneFile}
- [[ -f QAresults_Outer.root ]] && echo "qafile ${outputDir}/QAresults_Outer.root" >> ${doneFile}
echo "dir ${outputDir}" >> ${doneFile}
- summarizeLogs >> ${doneFile}
-
+ if summarizeLogs >> ${doneFile}; then
+ [[ -f AliESDs_Barrel.root ]] && echo "esd ${outputDir}/AliESDs_Barrel.root" >> ${doneFile}
+ [[ -f AliESDfriends_v1.root ]] && echo "calibfile ${outputDir}/AliESDfriends_v1.root" >> ${doneFile}
+ [[ -f QAresults_Barrel.root ]] && echo "qafile ${outputDir}/QAresults_Barrel.root" >> ${doneFile}
+ [[ -f QAresults_Outer.root ]] && echo "qafile ${outputDir}/QAresults_Outer.root" >> ${doneFile}
+ [[ -f QAresults_barrel.root ]] && echo "qafile ${outputDir}/QAresults_barrel.root" >> ${doneFile}
+ [[ -f QAresults_outer.root ]] && echo "qafile ${outputDir}/QAresults_outer.root" >> ${doneFile}
+ [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
+ else
+ if grep "qa_outer.log.*OK" ${doneFile} > /dev/null; then
+ [[ -f QAresults_Outer.root ]] && echo "qafile ${outputDir}/QAresults_Outer.root" >> ${doneFile}
+ [[ -f QAresults_outer.root ]] && echo "qafile ${outputDir}/QAresults_outer.root" >> ${doneFile}
+ fi
+ if grep "qa_barrel.log.*OK" ${doneFile} > /dev/null; then
+ [[ -f QAresults_Barrel.root ]] && echo "qafile ${outputDir}/QAresults_Barrel.root" >> ${doneFile}
+ [[ -f QAresults_barrel.root ]] && echo "qafile ${outputDir}/QAresults_barrel.root" >> ${doneFile}
+ fi
+ if grep "filtering.log.*OK" ${doneFile} > /dev/null; then
+ [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
+ fi
+ fi
+
[[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
return 0
-}
+)
goMergeCPass0()
-{
+(
#
# find the output files and merge them
#
runNumber=${4}
calibrationFilesToMerge=${5} #can be a non-existent file, will then be produced on the fly
shift 5
- parseConfig ${configFile} $@
+ if ! parseConfig ${configFile} "$@"; then return 1; fi
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
[[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
doneFile="${commonOutputPath}/meta/merge.cpass0.run${runNumber}.done"
#runpath=${PWD}/rundir_cpass0_Merge_${runNumber}
runpath=${outputDir}
- [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
- [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
+ #[[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
+ [[ ${reconstructInTemporaryDir} -eq 1 ]] && runpath=$(mktemp -d -t mergeCPass0.XXXXXX)
mkdir -p ${runpath}
[[ ! -d ${runpath} ]] && echo "not able to make the runpath ${runpath}" && touch ${doneFile} && return 1
- cd ${runpath}
+ if ! cd ${runpath}; then
+ echo "PWD=$PWD is not the runpath=${runpath}"
+ touch ${doneFile}
+ return 1
+ fi
logOutputDir=${runpath}
[[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
# copy files in case they are not already there
filesMergeCPass0=(
- "${commonOutputPath}/${calibrationFilesToMerge}"
- "${commonOutputPath}/OCDB.root"
- "${commonOutputPath}/localOCDBaccessConfig.C"
+ "${batchWorkingDirectory}/${calibrationFilesToMerge}"
+ "${batchWorkingDirectory}/OCDB.root"
+ "${batchWorkingDirectory}/localOCDBaccessConfig.C"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/mergeMakeOCDB.byComponent.sh"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/mergeByComponent.C"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/makeOCDB.C"
)
for file in ${filesMergeCPass0[*]}; do
[[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
+ [[ ${file##*/} =~ .*\.sh ]] && chmod +x ${file##*/}
done
sed -i '/.*root .*\.C/ s|\s*,\s*|,|g' *.sh
echo "${mergingScript} ${calibrationFilesToMerge} ${runNumber} local://./OCDB ${ocdbStorage}"
if [[ -n ${pretend} ]]; then
+ sleep ${pretendDelay}
touch CalibObjects.root
touch ocdb.log
touch merge.log
+ touch dcsTime.root
mkdir -p ./OCDB/TPC/Calib/TimeGain/
mkdir -p ./OCDB/TPC/Calib/TimeDrift/
touch ./OCDB/TPC/Calib/TimeGain/someCalibObject_0-999999_cpass0.root
touch ./OCDB/TPC/Calib/TimeDrift/otherCalibObject_0-999999_cpass0.root
else
./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" ${ocdbStorage}
- fi
+ #produce the calib trees for expert QA (dcsTime.root)
+ goMakeLocalOCDBaccessConfig ./OCDB
+ echo aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
+ aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
+ fi
+
### produce the output
#tar the produced OCDB for reuse
tar czf ${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz ./OCDB
- #produce the calib trees for expert QA (dcsTime.root)
- goMakeLocalOCDBaccessConfig ./OCDB
- echo aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
- aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
-
/bin/ls
#copy all to output dir
- cp -pf --recursive ${runpath}/* ${outputDir}
-
+ cp -pf -R ${runpath}/* ${outputDir}
+
if [[ -n ${generateMC} ]]; then
goPrintValues sim ${commonOutputPath}/meta/sim.run${runNumber}.list ${commonOutputPath}/meta/cpass0.job*.run${runNumber}.done
fi
#validate merging cpass0
cd ${outputDir}
touch ${doneFile}
- [[ -f CalibObjects.root ]] && echo "calibfile ${outputDir}/CalibObjects.root" >> ${doneFile}
- [[ -f dcsTime.root ]] && echo "dcsTree ${outputDir}/dcsTime.root" >> ${doneFile}
echo "dir ${outputDir}" >> ${doneFile}
- summarizeLogs >> ${doneFile}
+ if summarizeLogs >> ${doneFile}; then
+ [[ -f CalibObjects.root ]] && echo "calibfile ${outputDir}/CalibObjects.root" >> ${doneFile}
+ [[ -f dcsTime.root ]] && echo "dcsTree ${outputDir}/dcsTime.root" >> ${doneFile}
+ fi
[[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
return 0
-}
+)
goMergeCPass1()
-{
+(
#
# find the output files and merge them
#
runNumber=${4}
calibrationFilesToMerge=${5}
qaFilesToMerge=${6}
- shift 6
- parseConfig ${configFile} $@
+ filteredFilesToMerge=${7}
+ shift 7
+ if ! parseConfig ${configFile} "$@"; then return 1; fi
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
[[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
doneFile="${commonOutputPath}/meta/merge.cpass1.run${runNumber}.done"
#runpath=${PWD}/rundir_cpass1_Merge_${runNumber}
runpath=${outputDir}
- [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
- [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
+ #[[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
+ [[ ${reconstructInTemporaryDir} -eq 1 ]] && runpath=$(mktemp -d -t mergeCPass1.XXXXXX)
mkdir -p ${runpath}
[[ ! -d ${runpath} ]] && echo "not able to make the runpath ${runpath}" && touch ${doneFile} && return 1
- cd ${runpath}
+ if ! cd ${runpath}; then
+ echo "PWD=$PWD is not the runpath=${runpath}"
+ touch ${doneFile}
+ return 1
+ fi
logOutputDir=${runpath}
[[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
# copy files in case they are not already there
filesMergeCPass1=(
- "${commonOutputPath}/${calibrationFilesToMerge}"
- "${commonOutputPath}/${qaFilesToMerge}"
- "${commonOutputPath}/OCDB.root"
- "${commonOutputPath}/localOCDBaccessConfig.C"
+ "${batchWorkingDirectory}/${calibrationFilesToMerge}"
+ "${batchWorkingDirectory}/${qaFilesToMerge}"
+ "${batchWorkingDirectory}/OCDB.root"
+ "${batchWorkingDirectory}/localOCDBaccessConfig.C"
"${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz"
- "${commonOutputPath}/QAtrain_duo.C"
+ "${batchWorkingDirectory}/QAtrain_duo.C"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/mergeMakeOCDB.byComponent.sh"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/mergeByComponent.C"
"${ALICE_ROOT}/PWGPP/CalibMacros/CPass1/makeOCDB.C"
)
for file in ${filesMergeCPass1[*]}; do
[[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
+ [[ ${file##*/} =~ .*\.sh ]] && chmod +x ${file##*/}
done
sed -i '/.*root .*\.C/ s|\s*,\s*|,|g' *.sh
#merge calibration
chmod u+x ${mergingScript}
mkdir -p OCDB
- if [[ ! -f ${calibrationFilesToMerge} ]]; then
- echo "/bin/ls -1 ${outputDir}/*/${calibrationOutputFileName} > ${calibrationFilesToMerge}"
- /bin/ls -1 ${outputDir}/*/${calibrationOutputFileName} 2>/dev/null > ${calibrationFilesToMerge}
- fi
- echo "${mergingScript} ${calibrationFilesToMerge} ${runNumber} local://./OCDB ${ocdbStorage}"
- if [[ -n ${pretend} ]]; then
- touch CalibObjects.root
- touch ocdb.log
- touch merge.log
- touch cpass1.localOCDB.${runNumber}.tgz
- else
- ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" ${ocdbStorage}
+ #if not provided, create the lists of files to merge
+ if [[ ! -f ${filteredFilesToMerge} ]]; then
+ echo "/bin/ls -1 ${outputDir}/*/FilterEvents_Trees.root > ${filteredFilesToMerge}"
+ /bin/ls -1 ${outputDir}/*/FilterEvents_Trees.root 2>/dev/null > ${filteredFilesToMerge}
+ fi
+ if [[ ! -f ${calibrationFilesToMerge} ]]; then
+ echo "/bin/ls -1 ${outputDir}/*/AliESDfriends_v1.root > ${calibrationFilesToMerge}"
+ /bin/ls -1 ${outputDir}/*/AliESDfriends_v1.root 2>/dev/null > ${calibrationFilesToMerge}
fi
-
- tar czf ${commonOutputPath}/meta/cpass1.localOCDB.${runNumber}.tgz ./OCDB
-
- #merge QA
- [[ -n ${AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF} ]] && export AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF
- [[ -n ${AliAnalysisTaskFilteredTree_fLowPtV0DownscaligF} ]] && export AliAnalysisTaskFilteredTree_fLowPtV0DownscaligF
-
if [[ ! -f ${qaFilesToMerge} ]]; then
#find the files, but only store the directories (QAtrain_duo.C requires this)
- echo "/bin/ls -1 ${outputDir}/*/${qaOutputFileName} | while read x; do echo ${x%/*}; done | sort | uniq > ${qaFilesToMerge}"
- eval "/bin/ls -1 ${outputDir}/*/${qaOutputFileName}" | while read x; do echo ${x%/*}; done | sort | uniq > ${qaFilesToMerge}
+ echo "/bin/ls -1 ${outputDir}/*/QAresults*.root | while read x; do echo ${x%/*}; done | sort | uniq > ${qaFilesToMerge}"
+ /bin/ls -1 ${outputDir}/*/QAresults*.root | while read x; do echo ${x%/*}; done | sort | uniq > ${qaFilesToMerge}
fi
- #do the merge
- #echo aliroot -l -b -q "merge.C(\"${qaFilesToMerge}\",\"\",kFALSE,\"${qaMergedOutputFileName}\")"
- echo aliroot -b -q "QAtrain_duo.C(\"_barrel\",${runNumber},\"${qaFilesToMerge}\",1,\"${ocdbStorage}\")"
+ echo "${mergingScript} ${calibrationFilesToMerge} ${runNumber} local://./OCDB ${ocdbStorage}"
if [[ -n ${pretend} ]]; then
+ sleep ${pretendDelay}
+ touch ocdb.log
+ touch cpass1.localOCDB.${runNumber}.tgz
touch ${qaMergedOutputFileName}
touch merge.log
touch trending.root
+ touch FilterEvents_Trees.root
+ touch CalibObjects.root
+ touch dcsTime.root
+ touch ${qaMergedOutputFileName}
+ mkdir -p OCDB
else
+ ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" ${ocdbStorage}
+
+ #merge QA (and filtered trees)
+ [[ -n ${AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF} ]] && export AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF
+ [[ -n ${AliAnalysisTaskFilteredTree_fLowPtV0DownscaligF} ]] && export AliAnalysisTaskFilteredTree_fLowPtV0DownscaligF
+
+ #echo aliroot -l -b -q "merge.C(\"${qaFilesToMerge}\",\"\",kFALSE,\"${qaMergedOutputFileName}\")"
+ echo aliroot -b -q "QAtrain_duo.C(\"_barrel\",${runNumber},\"${qaFilesToMerge}\",1,\"${ocdbStorage}\")"
#aliroot -l -b -q "merge.C(\"${qaFilesToMerge}\",\"\",kFALSE,\"${qaMergedOutputFileName}\")"
aliroot -b -q "QAtrain_duo.C(\"_barrel\",${runNumber},\"${qaFilesToMerge}\",1,\"${ocdbStorage}\")" > mergeQA.log
mv QAresults_barrel.root ${qaMergedOutputFileName}
mv trending_barrel.root trending.root
+
+ #merge filtered trees
+ echo aliroot -l -b -q "merge.C(\"${qaFilesToMerge}\",\"\",kFALSE,\"${qaMergedOutputFileName}\")"
+ aliroot -l -b -q "merge.C(\"${filteredFilesToMerge}\",\"\",kFALSE,\"FilterEvents_Trees.root\")" > mergeFilteredTrees.log
+
+ #produce the calib trees for expert QA
+ echo aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
+ aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")" > calibTree.log
fi
-
- #produce the calib trees for expert QA
- echo aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
- aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")"
+
+ tar czf ${commonOutputPath}/meta/cpass1.localOCDB.${runNumber}.tgz ./OCDB
/bin/ls
#copy all to output dir
- cp -pf --recursive ${runpath}/* ${outputDir}
+ cp -pf -R ${runpath}/* ${outputDir}
#validate merge cpass1
cd ${outputDir}
touch ${doneFile}
- [[ -f CalibObjects.root ]] && echo "calibfile ${outputDir}/CalibObjects.root" >> ${doneFile}
- [[ -f ${qaMergedOutputFileName} ]] && echo "qafile ${outputDir}/${qaMergedOutputFileName}" >> ${doneFile}
- [[ -f trending.root ]] && echo "trendingfile ${outputDir}/trending.root" >> ${doneFile}
- [[ -f dcsTime.root ]] && echo "dcsTree ${outputDir}/dcsTime.root" >> ${doneFile}
echo "dir ${outputDir}" >> ${doneFile}
- summarizeLogs >> ${doneFile}
+ if summarizeLogs >> ${doneFile}; then
+ [[ -f CalibObjects.root ]] && echo "calibfile ${outputDir}/CalibObjects.root" >> ${doneFile}
+ [[ -f ${qaMergedOutputFileName} ]] && echo "qafile ${outputDir}/${qaMergedOutputFileName}" >> ${doneFile}
+ [[ -f trending.root ]] && echo "trendingfile ${outputDir}/trending.root" >> ${doneFile}
+ [[ -f dcsTime.root ]] && echo "dcsTree ${outputDir}/dcsTime.root" >> ${doneFile}
+ [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
+ else
+ if grep "mergeQA.log.*OK" ${doneFile} > /dev/null; then
+ [[ -f ${qaMergedOutputFileName} ]] && echo "qafile ${outputDir}/${qaMergedOutputFileName}" >> ${doneFile}
+ fi
+ if grep "mergeFilteredTrees.log.*OK" ${doneFile} > /dev/null; then
+ [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
+ fi
+ fi
[[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
return 0
-}
+)
goMerge()
-{
+(
#generic root merge using CPass1 merge.C script
inputList=${1}
outputFile=${2}
- configFile=${3-"becnhmark.config"}
+ configFile=${3-"benchmark.config"}
shift 3
- parseConfig ${configFile} $@
+ if ! parseConfig ${configFile} "$@"; then return 1; fi
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
[[ ! -f ${inputList} ]] && echo "inputList ${inputList} does not exist!" && return 1
[[ ! -f ${configFile} ]] && echo "configFile ${configFile} does not exist!" && return 1
rm -f ${outputFile}
aliroot -b -q "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/merge.C(\"${inputList}\",\"\",kFALSE,\"${outputFile}\")" > merge_${inputList}.log
return 0
-}
+)
goSubmitMakeflow()
{
inputFileList=${2}
configFile=${3}
shift 3
- extraOpts="$@"
- parseConfig ${configFile} ${extraOpts}
+ extraOpts=("$@")
+ if ! parseConfig ${configFile} "${extraOpts[@]}"; then return 1; fi
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
[[ -z ${configFile} ]] && configFile="benchmark.config"
[[ ! -f ${configFile} ]] && echo "no config file found (${configFile})" && return 1
- #create the directopry for the metadata
- mkdir meta
-
if [[ ! $(which makeflow &>/dev/null) && -n ${makeflowPath} ]]; then
echo "setting the makflow path from the config: "
echo " export PATH=${makeflowPath}:${PATH}"
export PATH=${makeflowPath}:${PATH}
fi
+ #create the common output dir and the meta dir
+ commonOutputPath=${baseOutputDirectory}/${productionID}
+ if [[ -d ${commonOutputPath} ]]; then
+ echo "output dir ${commonOutputPath} exists!"
+ #return 1
+ else
+ mkdir -p ${commonOutputPath}
+ fi
+ mkdir -p ${commonOutputPath}/meta
+
+ self=${0}
+ #if which greadlink; then self=$(greadlink -f "${0}"); fi
+
+ #for reference copy the setup to the output dir
+ cp ${self} ${commonOutputPath}
+ cp ${configFile} ${commonOutputPath}
+ cp ${inputList} ${commonOutputPath}
+
#submit - use makeflow if available, fall back to old stuff when makeflow not there
if which makeflow; then
- goGenerateMakeflow ${productionID} ${inputFileList} ${configFile} "${extraOpts}" > benchmark.makeflow
+ goGenerateMakeflow ${productionID} ${inputFileList} ${configFile} "${extraOpts[@]}" commonOutputPath=${commonOutputPath} > benchmark.makeflow
makeflow ${makeflowOptions} benchmark.makeflow
cd ../
}
goGenerateMakeflow()
-{
+(
#generate the makeflow file
+ [[ $# -lt 3 ]] && echo "args: id inputFileList configFile" && return 1
productionID=${1}
inputFileList=${2}
configFile=${3}
shift 3
- extraOpts="$@"
- parseConfig ${configFile} ${extraOpts}
+ extraOpts=("$@")
+
+ #batch systems/makeflow sometimes handle spaces in arguments poorly, so encode them
+ for (( i=0;i<${#extraOpts[@]};i++ )); do
+ extraOpts[i]=$(encSpaces "${extraOpts[i]}")
+ done
+ extraOpts+=("encodedSpaces=1")
+
+ if ! parseConfig ${configFile} "${extraOpts[@]}" &>/dev/null; then return 1; fi
+
+ #extra safety
+ if [[ -z ${commonOutputPath} ]]; then
+ commonOutputPath=${baseOutputDirectory}/${productionID}
+ extraOpts=( "${extraOpts[@]}" "commonOutputPath=${commonOutputPath}" )
+ fi
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
[[ -z ${configFile} ]] && configFile="benchmark.config"
[[ ! -f ${configFile} ]] && echo "no config file found (${configFile})" && return 1
- commonOutputPath=${baseOutputDirectory}/${productionID}
-
#these files will be made a dependency - will be copied to the working dir of the jobs
declare -a copyFiles
inputFiles=(
#create the makeflow file
[[ -n ${batchFlags} ]] && echo "BATCH_OPTIONS = ${batchFlags}"
- declare -a arr_cpass1_final
- listOfRuns[0]=${runNumber}
- [[ -z ${runNumber} ]] && listOfRuns=($(while read x; do guessRunNumber ${x}; done < ${inputFileList} | sort | uniq))
- runindex=0
- for runNumber in ${listOfRuns[*]}; do
+ declare -A arr_cpass0_merged arr_cpass1_merged
+ declare -A arr_cpass0_calib_list arr_cpass1_calib_list
+ declare -A arr_cpass1_QA_list arr_cpass1_ESD_list arr_cpass1_filtered_list
+ declare -A arr_cpass0_profiled_outputs
+ declare -A listOfRuns
+ [[ -n ${runNumber} ]] && listOfRuns[${runNumber}]=1
+ while read x; do tmpRun=$(guessRunNumber ${x}); [[ -n ${tmpRun} ]] && listOfRuns[${tmpRun}]=1; done < ${inputFileList}
+ for runNumber in "${!listOfRuns[@]}"; do
[[ -z ${runNumber} ]] && continue
[[ ! ${runNumber} =~ ^[0-9]*[0-9]$ ]] && continue
- unset arr_cpass0_outputs_onerun
- unset arr_cpass1_outputs_onerun
- declare -a arr_cpass0_outputs_onerun
- declare -a arr_cpass1_outputs_onerun
+ unset arr_cpass0_outputs
+ unset arr_cpass1_outputs
+ declare -a arr_cpass0_outputs
+ declare -a arr_cpass1_outputs
jobindex=0
+ inputFile=""
while read inputFile; do
currentDefaultOCDB=${defaultOCDB}
[[ -z ${autoOCDB} ]] && autoOCDB=1
fi
#CPass0
- arr_cpass0_outputs_onerun[${jobindex}]="meta/cpass0.job${jobindex}.run${runNumber}.done"
- echo "${arr_cpass0_outputs_onerun[${jobindex}]} : benchmark.sh ${configFile} ${copyFiles[@]}"
- echo " ${alirootEnv} ./benchmark.sh CPass0 ${commonOutputPath}/000${runNumber}/cpass0 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex} ${extraOpts}"
- echo
+ arr_cpass0_outputs[${jobindex}]="${commonOutputPath}/meta/cpass0.job${jobindex}.run${runNumber}.done"
+ echo "${arr_cpass0_outputs[${jobindex}]} : benchmark.sh ${configFile} ${copyFiles[@]}"
+ echo " ${alirootEnv} ./benchmark.sh CPass0 ${commonOutputPath}/000${runNumber}/cpass0 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex} ${extraOpts[@]}"" "
#CPass1
- arr_cpass1_outputs_onerun[${jobindex}]="meta/cpass1.job${jobindex}.run${runNumber}.done"
- echo "${arr_cpass1_outputs_onerun[${jobindex}]} : benchmark.sh ${configFile} meta/cpass0.localOCDB.${runNumber}.tgz ${copyFiles[@]}"
- echo " ${alirootEnv} ./benchmark.sh CPass1 ${commonOutputPath}/000${runNumber}/cpass1 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex} ${extraOpts}"
- echo
+ arr_cpass1_outputs[${jobindex}]="${commonOutputPath}/meta/cpass1.job${jobindex}.run${runNumber}.done"
+ echo "${arr_cpass1_outputs[${jobindex}]} : benchmark.sh ${configFile} ${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz ${copyFiles[@]}"
+ echo " ${alirootEnv} ./benchmark.sh CPass1 ${commonOutputPath}/000${runNumber}/cpass1 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex} ${extraOpts[@]}"" "
((jobindex++))
done< <(grep "/000${runNumber}/" ${inputFileList})
#CPass0 list of Calib files to merge
- arr_cpass0_calib_list[${runindex}]="meta/cpass0.calib.run${runNumber}.list"
- echo "${arr_cpass0_calib_list[${runindex}]} : benchmark.sh ${arr_cpass0_outputs_onerun[*]}"
- echo " ./benchmark.sh PrintValues calibfile ${arr_cpass0_calib_list[${runindex}]} ${arr_cpass0_outputs_onerun[*]}"
+ arr_cpass0_calib_list[${runNumber}]="${commonOutputPath}/meta/cpass0.calib.run${runNumber}.list"
+ echo "${arr_cpass0_calib_list[${runNumber}]} : benchmark.sh ${arr_cpass0_outputs[*]}"
+ echo " ./benchmark.sh PrintValues calibfile ${arr_cpass0_calib_list[${runNumber}]} ${arr_cpass0_outputs[*]}"
echo
#CPass0 merging
- arr_cpass0_final[${runindex}]="meta/merge.cpass0.run${runNumber}.done"
- echo "meta/cpass0.localOCDB.${runNumber}.tgz ${arr_cpass0_final[${runindex}]} : benchmark.sh ${configFile} ${arr_cpass0_calib_list[${runindex}]} ${copyFiles[@]}"
- echo " ${alirootEnv} ./benchmark.sh MergeCPass0 ${commonOutputPath}/000${runNumber}/cpass0 ${currentDefaultOCDB} ${configFile} ${runNumber} ${arr_cpass0_calib_list[${runindex}]} ${extraOpts}"
- echo
+ arr_cpass0_merged[${runNumber}]="${commonOutputPath}/meta/merge.cpass0.run${runNumber}.done"
+ echo "${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz ${arr_cpass0_merged[${runNumber}]} : benchmark.sh ${configFile} ${arr_cpass0_calib_list[${runNumber}]} ${copyFiles[@]}"
+ echo " ${alirootEnv} ./benchmark.sh MergeCPass0 ${commonOutputPath}/000${runNumber}/cpass0 ${currentDefaultOCDB} ${configFile} ${runNumber} ${arr_cpass0_calib_list[${runNumber}]} ${extraOpts[@]}"" "
- #CPass1 list of Calib/QA files to merge
- # the trick is to have the string "Stage.txt" in the file name of the list of directories with QA output to trigger
- # the production of the trending tree (only then the task->Finish() will be called in QAtrain_duo.C, on the grid
+ #CPass1 list of Calib/QA/ESD/filtered files
+ # the trick with QA is to have the string "Stage.txt" in the file name of the list of directories with QA output to trigger
+ # the production of the QA trending tree (only then the task->Finish() will be called in QAtrain_duo.C, on the grid
# this corresponds to the last merging stage)
- arr_cpass1_calib_list[${runindex}]="meta/cpass1.calib.run${runNumber}.list"
- echo "${arr_cpass1_calib_list[${runindex}]} : benchmark.sh ${arr_cpass1_outputs_onerun[*]}"
- echo " ./benchmark.sh PrintValues calibfile ${arr_cpass1_calib_list[${runindex}]} ${arr_cpass1_outputs_onerun[*]};"
+ arr_cpass1_QA_list[${runNumber}]="${commonOutputPath}/meta/cpass1.QA.run${runNumber}.lastMergingStage.txt.list"
+ echo "${arr_cpass1_QA_list[${runNumber}]}: benchmark.sh ${arr_cpass1_outputs[*]}"
+ echo " ./benchmark.sh PrintValues dir ${arr_cpass1_QA_list[${runNumber}]} ${arr_cpass1_outputs[*]}"
echo
- arr_cpass1_QA_list[${runindex}]="meta/cpass1.QA.run${runNumber}.lastMergingStage.txt.list"
- echo "${arr_cpass1_QA_list[${runindex}]}: benchmark.sh ${arr_cpass1_outputs_onerun[*]}"
- echo " ./benchmark.sh PrintValues dir ${arr_cpass1_QA_list[${runindex}]} ${arr_cpass1_outputs_onerun[*]}"
+ arr_cpass1_calib_list[${runNumber}]="${commonOutputPath}/meta/cpass1.calib.run${runNumber}.list"
+ echo "${arr_cpass1_calib_list[${runNumber}]} : benchmark.sh ${arr_cpass1_outputs[*]}"
+ echo " ./benchmark.sh PrintValues calibfile ${arr_cpass1_calib_list[${runNumber}]} ${arr_cpass1_outputs[*]};"
echo
-
- #CPass1 merging
- arr_cpass1_final[${runindex}]="meta/merge.cpass1.run${runNumber}.done"
- echo "meta/cpass1.localOCDB.${runNumber}.tgz ${arr_cpass1_final[${runindex}]} : benchmark.sh ${configFile} ${arr_cpass1_calib_list[${runindex}]} ${arr_cpass1_QA_list[${runindex}]} ${copyFiles[@]}"
- echo " ${alirootEnv} ./benchmark.sh MergeCPass1 ${commonOutputPath}/000${runNumber}/cpass1 ${currentDefaultOCDB} ${configFile} ${runNumber} ${arr_cpass1_calib_list[${runindex}]} ${arr_cpass1_QA_list[${runindex}]} ${extraOpts}"
+ arr_cpass1_ESD_list[${runNumber}]="${commonOutputPath}/meta/cpass1.ESD.run${runNumber}.list"
+ echo "${arr_cpass1_ESD_list[${runNumber}]} : benchmark.sh ${arr_cpass1_outputs[*]}"
+ echo " ./benchmark.sh PrintValues esd ${arr_cpass1_ESD_list[${runNumber}]} ${arr_cpass1_outputs[*]}"
echo
-
- arr_cpass1_ESD_list[${runindex}]="meta/cpass1.ESD.run${runNumber}.list"
- echo "${arr_cpass1_ESD_list[${runindex}]} : benchmark.sh ${arr_cpass1_outputs_onerun[*]}"
- echo " ./benchmark.sh PrintValues esd ${arr_cpass1_ESD_list[${runindex}]} ${arr_cpass1_outputs_onerun[*]}"
-
- if [ ${runESDfiltering} -eq 1 ]; then
- arr_cpass1_filtering[${runindex}]="meta/filtering.cpass1.run${runNumber}.done"
- echo "${arr_cpass1_filtering[${runindex}]} : benchmark.sh ${configFile} ${arr_cpass1_ESD_list[${runindex}]}"
- echo " ${alirootEnv} ./benchmark.sh MakeFilteredTrees ${commonOutputPath}/000${runNumber}/cpass1 ${runNumber} ${arr_cpass1_ESD_list[${runindex}]} ${filteringFactorHighPt} ${filteringFactorV0s} ${currentDefaultOCDB} 1000000 0 10000000 0 ${configFile} AliESDs_Barrel.root ${extraOpts}"
+ arr_cpass1_filtered_list[${runNumber}]="${commonOutputPath}/meta/cpass1.filtered.run${runNumber}.list"
+ echo "${arr_cpass1_filtered_list[${runNumber}]} : benchmark.sh ${arr_cpass1_outputs[*]}"
+ echo " ./benchmark.sh PrintValues filteredTree ${arr_cpass1_filtered_list[${runNumber}]} ${arr_cpass1_outputs[*]}"
+ echo
+
+ #CPass1 merging
+ arr_cpass1_merged[${runNumber}]="${commonOutputPath}/meta/merge.cpass1.run${runNumber}.done"
+ echo "${commonOutputPath}/meta/cpass1.localOCDB.${runNumber}.tgz ${arr_cpass1_merged[${runNumber}]} : benchmark.sh ${configFile} ${arr_cpass1_calib_list[${runNumber}]} ${arr_cpass1_QA_list[${runNumber}]} ${copyFiles[@]}"
+ echo " ${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}]} ${extraOpts[@]}"" "
+
+ #CPass0 wrapped in a profiling tool (valgrind,....)
+ if [[ -n ${profilingCommand} ]]; then
+ inputFile=$(grep -m1 "${runNumber}/" ${inputFileList})
+ [[ -z ${nEventsProfiling} ]] && nEventsProfiling=2
+ currentDefaultOCDB=$(setYear ${inputFile} ${defaultOCDB})
+ jobindex="profiling"
+
+ arr_cpass0_profiled_outputs[${runNumber}]="${commonOutputPath}/meta/cpass0.job${jobindex}.run${runNumber}.done"
+ echo "${arr_cpass0_profiled_outputs[${runNumber}]} : benchmark.sh ${configFile} ${copyFiles[@]}"
+ profilingCommand=$(encSpaces "${profilingCommand}")
+ echo " ${alirootEnv} ./benchmark.sh CPass0 ${commonOutputPath}/000${runNumber}/${jobindex} ${inputFile} ${nEventsProfiling} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex} ${extraOpts[@]} useProfilingCommand=${profilingCommand}"
fi
- ((runindex++))
- done
+ done #runs
#Summary
- echo "summary.log : benchmark.sh ${configFile} ${arr_cpass1_final[*]} ${arr_cpass1_filtering[*]}"
- echo " LOCAL ./benchmark.sh MakeSummary ${configFile}"
+ echo "${commonOutputPath}/summary.log : benchmark.sh ${configFile} ${arr_cpass1_merged[*]}"
+ echo " ${alirootEnv} ./benchmark.sh MakeSummary ${configFile} ${extraOpts[@]}"
echo
return 0
-}
+)
goPrintValues()
-{
+(
#print the values given the key from any number of files (store in output file on second argument)
if [[ $# -lt 3 ]]; then
echo "goPrintValues key outputFile inputFiles"
shift 2 #remove 2 first arguments from arg list to only pass the input files to awk
awk -v key=${key} '$0 ~ key" " {print $2}' "$@" | tee ${outputFile}
return 0
-}
+)
goCreateQAplots()
-{
+(
umask 0002
mergedQAfileList=${1}
productionID=${2}
outputDir=${3}
configFile=${4}
shift 4
- parseConfig ${configFile} ${@}
+ if ! parseConfig ${configFile} ${@}; then return 1; fi
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
+
[[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
[[ -z ${logOutputDir} ]] && logOutputDir=${PWD}
- [[ -z ${dontRedirectStdOutToLog} ]] && exec 2>&1 > ${logOutputDir}/makeQAplots.log
+ [[ -z ${dontRedirectStdOutToLog} ]] && exec &> ${logOutputDir}/makeQAplots.log
echo "${0} $*"
olddir=${PWD}
mkdir -p ${outputDir}
cd ${outputDir}
- [[ ! "${PWD}" = "${outputDir}" ]] && echo "cannot make ${outputDir}... exiting" && return 1
+ [[ ! "${PWD}" =~ "${outputDir}" ]] && echo "PWD is not equal to outputDir=${outputDir}" && cd ${olddir} && return 1
- echo ${ALICE_ROOT}/PWGPP/QA/scripts/runQA.sh inputList=${mergedQAfileList}
- ${ALICE_ROOT}/PWGPP/QA/scripts/runQA.sh inputList=${mergedQAfileList}
+ ${ALICE_ROOT}/PWGPP/QA/scripts/runQA.sh inputList="${mergedQAfileList}" inputListHighPtTrees="${filteringList}"
cd ${olddir}
return 0
-}
+)
goTest()
-{
- umask 0002
- exec 2>&1
- exec > >(tee test.log)
- echo "$@"
- echo something
- return 0
-}
+(
+ echo AA
+)
alirootInfo()
-{
+(
umask 0002
# save aliroot repository info
[[ -z "${ALICE_ROOT}" ]] && return 1
echo "\${ROOTSYS}=${ROOTSYS}"
echo "\${PATH}=${PATH}"
echo "\${LD_LIBRARY_PATH}=${LD_LIBRARY_PATH}"
+ echo
pushd ${PWD}
cd ${ALICE_ROOT}
- echo
currentBranch=$(git rev-parse --abbrev-ref HEAD)
git status
git diff ${currentBranch}
popd
return 0
-}
+)
setYear()
-{
+(
#set the year
# ${1} - year to be set
# ${2} - where to set the year
[[ ${year1} -ne ${year2} && -n ${year2} && -n ${year1} ]] && path=${2/\/${year2}\//\/${year1}\/}
echo ${path}
return 0
-}
+)
guessPeriod()
-{
+(
#guess the period from the path, pick the rightmost one
local IFS="/"
declare -a path=( ${1} )
done
echo ${period}
return 0
-}
+)
guessYear()
-{
+(
#guess the year from the path, pick the rightmost one
local IFS="/"
declare -a path=( ${1} )
done
echo ${year}
return 0
-}
+)
guessRunNumber()
-{
+(
#guess the run number from the path, pick the rightmost one
#works for /path/foo/000123456/bar/...
#and /path/foo.run123456.bar
for ((x=${dirDepth}-1;x>=0;x--)); do
local field=${path[${x}]}
field=${field/run/000}
- [[ ${field} =~ ^000[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && runNumber=${field#000} && break
+ [[ ${field} =~ [0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && runNumber=${field#000} && break
done
echo ${runNumber}
return 0
-}
+)
validateLog()
-{
+(
log=${1}
errorConditions=(
'There was a crash'
'AliFatal'
'core dumped'
'\.C.*error:.*\.h: No such file'
+ 'line.*Aborted'
)
warningConditions=(
fi
return 0
-}
+)
summarizeLogs()
-{
+(
#print a summary of logs
logFiles=(
"*.log"
if [[ ${validationStatus} -eq 0 ]]; then
#in pretend mode randomly report an error in rec.log some cases
if [[ -n ${pretend} && "${log}" == "rec.log" ]]; then
- [[ $(( ${RANDOM}%2 )) -ge 1 ]] && echo "${finallog} BAD random error" || echo "${finallog} OK"
+ #[[ $(( ${RANDOM}%2 )) -ge 1 ]] && echo "${finallog} BAD random error" || echo "${finallog} OK"
+ echo "${finallog} OK"
else
echo "${finallog} OK"
fi
elif [[ ${validationStatus} -eq 1 ]]; then
echo "${finallog} BAD ${errorSummary}"
+ logstatus=1
elif [[ ${validationStatus} -eq 2 ]]; then
echo "${finallog} OK MWAH ${errorSummary}"
fi
done < <(/bin/ls ${PWD}/*/core 2>/dev/null; /bin/ls ${PWD}/core 2>/dev/null)
return ${logstatus}
-}
+)
spitOutLocalOCDBaccessConfig()
{
local tempLocalOCDB=""
if [[ -f localOCDBaccessConfig.C ]]; then
- tempLocalOCDB=$(mktemp)
+ tempLocalOCDB=$(mktemp -t tempLocalOCDB.XXXXXX)
echo "egrep "SetSpecificStorage" localOCDBaccessConfig.C > ${tempLocalOCDB}"
egrep "SetSpecificStorage" localOCDBaccessConfig.C > ${tempLocalOCDB}
fi
}
goMakeFilteredTrees()
-{
+(
outputDir=${1}
runNumber=${2}
#get path to input list
configFile=${11-"benchmark.config"}
esdFileName=${12-"AliESDs_Barrel.root"}
shift 12
- parseConfig ${configFile} $@
+ if ! parseConfig ${configFile} "$@"; then return 1; fi
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
- commonOutputPath=${PWD}
+ [[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
doneFile=${commonOutputPath}/meta/filtering.cpass1.run${runNumber}.done
- runpath=${commonOutputPath}/rundir_filtering_run${runNumber}
-
- [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
-
- mkdir -p ${outputDir}
- mkdir -p ${runpath}
-
- cd ${runpath}
-
cat > filtering.log << EOF
goMakeFilteredTrees config:
runpath=${runpath}
offsetEvent=$offsetEvent
configFile=$configFile
esdFileName=$esdFileName
+ inputListfiles=$inputListfiles
+ doneFile=$doneFile
EOF
+ #runpath=${outputDir}
+ #[[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
+ #[[ ${reconstructInTemporaryDir} -eq 1 ]] && runpath=$(mktemp -d -t goMakeFilteredTrees.XXXXXX)
+ #mkdir -p ${outputDir}
+ #mkdir -p ${runpath}
+ #if ! cd ${runpath}; then
+ # echo "PWD=$PWD is not the runpath=${runpath}"
+ # touch ${doneFile}
+ # return 1
+ #fi
+
if [[ -z ${pretend} ]];then
aliroot -l -b -q "${ALICE_ROOT}/PWGPP/macros/runFilteringTask.C(\"${inputListfiles}\",${filterT},${filterV},\"${OCDBpath}\",${maxFiles},${offsetFile},${maxEvents},${offsetEvent},\"${esdFileName}\")" &>> filtering.log
else
+ sleep ${pretendDelay}
touch filtering.log FilterEvents_Trees.root
fi
pwd
/bin/ls
touch ${doneFile}
summarizeLogs >> ${doneFile}
- echo mv -f * ${outputDir}
- mv -f * ${outputDir}
- [[ -f ${outputDir}/FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
- cd ${commonOutputPath}
- [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
+
+ #echo mv -f * ${outputDir}
+ #mv -f * ${outputDir}
+ #[[ -f ${outputDir}/FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
+ #cd ${commonOutputPath}
+ #[[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
+
return 0
-}
+)
submit()
{
umask 0002
- [[ $# -ne 6 ]] && echo "6 args needed, you supplied $#" && return 1
+ [[ $# -lt 5 ]] && echo "at least 5 args needed, you supplied $#" && return 1
JobID=${1}
startID=${2}
endID=${3}
waitForJOBID=${4}
command=${5}
- commandArgs=${6}
+ shift 5
+ local commandArgs=("$@")
+
+ #add quote strings around the extra arguments
+ for ((i=0; i<${#commandArgs[@]}; i++)); do
+ commandArgs[i]=\"${commandArgs[i]}\"
+ done
[[ -z ${waitForJOBID} ]] && waitForJOBID=0
else
#new SGE farm
if [[ ${waitForJOBID} =~ "000" ]]; then
- echo ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" ${commandArgs}
- ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" ${commandArgs}
+ echo ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" "${commandArgs[@]}"
+ ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" "${commandArgs[@]}"
else
- 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}
- ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -hold_jid "${waitForJOBID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" ${commandArgs}
+ 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[@]}"
+ ${batchCommand} ${batchFlags} -wd ${commonOutputPath} -b y -v commonOutputPath -N "${JobID}" -t "${startID}-${endID}" -hold_jid "${waitForJOBID}" -e "${commonOutputPath}/logs/" -o "${commonOutputPath}/logs/" "${command}" "${commandArgs[@]}"
fi
fi
return 0
productionID=${1}
inputList=${2}
configFile=${3:-"benchmark.config"}
- configFile=$(readlink -f ${configFile})
+ #if which greadlink; then configFile=$(greadlink -f ${configFile}); fi
shift 3
- extraOpts="$@"
- parseConfig ${configFile} ${extraOpts}
+ extraOpts=("$@")
+ if ! parseConfig ${configFile} "${extraOpts[@]}"; then return 1; fi
+
+ #batch systems/makeflow sometimes handle spaces in arguments poorly, so encode them
+ for (( i=0;i<${#extraOpts[@]};i++ )); do
+ extraOpts[i]=$(encSpaces "${extraOpts[i]}")
+ done
+ extraOpts+=("encodedSpaces=1")
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
#redirect all output to submit.log
echo "redirecting all output to ${PWD}/submit_${productionID//"/"/_}.log"
echo "Using Config File: '${configFile}'"
fi
- # and print the configuration
- [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
+ [[ ! -f ${alirootEnv} ]] && echo "alirootEnv script ${alirootEnv} not found!..." && return 1
#move the script, config and some other stuff to ${commonOutputPath} first, then use them from there
- self=$(readlink -f "${0}")
+ self=${0}
+ #if which greadlink; then self=$(greadlink -f "${0}"); fi
configPath=$(dirname ${configFile})
export commonOutputPath=${baseOutputDirectory}/${productionID}
inputList=${commonOutputPath}/${inputList##*/}
#convert to absolut pathnames
- inputList=$(readlink -f "${inputList}")
+ #if which greadlink; then inputList=$(greadlink -f "${inputList}"); fi
#make list of runs
if [[ -z ${runNumber} ]]; then
listOfRuns=($(while read x; do guessRunNumber ${x}; done < ${inputList} | sort | uniq))
listOfRuns=${runNumber}
fi
- alirootSource=$(readlink -f "${alirootSource}")
+ #if which greadlink; then alirootSource=$(greadlink -f "${alirootSource}"); fi
echo ""
echo "### BEGIN CONFIGURATION ###"
echo " productionID: ${productionID}"
echo " batchCommand: ${batchCommand}"
echo " batchFlags: ${batchFlags}"
- echo " alirootSource: ${alirootSource}"
- echo " ALICE_ROOT: ${ALICE_ROOT}"
- echo " ALIROOT_RELEASE: ${ALICE_RELEASE}"
+ echo " alirootEnv: ${alirootEnv}"
+ ${alirootEnv} echo ' ALICE_ROOT: ${ALICE_ROOT}'
+ ${alirootEnv} echo ' ALIROOT_RELEASE: ${ALICE_RELEASE}'
echo " inputList: ${inputList}"
echo " configPath: ${configPath}"
echo " commonOutputPath: ${commonOutputPath}"
JOBfilterESDcpass1="fp1_${JOBpostfix}"
LASTJOB="000"
- oneInputFile=$(egrep -m1 "${runNumber}\/" ${inputList})
+ oneInputFile=$(egrep -m1 "${runNumber}/" ${inputList})
currentDefaultOCDB=${defaultOCDB}
[[ -z ${autoOCDB} ]] && autoOCDB=1
###############################################################################
#run one chunk with valgrind:
- if [[ -n ${runValgrind} ]]; then
- [[ -z ${nEventsValgrind} ]] && nEventsValgrind=2
- [[ -z ${valgrindCommand} ]] && valgrindCommand="/usr/bin/valgrind --tool=callgrind --num-callers=40 -v --trace-children=yes"
- submit "valgrind" 1 1 000 "${alirootEnv} ${self}" "CPass0 ${commonOutputPath}/000${runNumber}/valgrind ${oneInputFile} ${nEventsValgrind} ${currentDefaultOCDB} ${configFile} ${runNumber} valgrind valgrindCommand=${valgrindCommand} ${extraOpts}"
+ if [[ -n ${profilingCommand} ]]; then
+ [[ -z ${nEventsProfiling} ]] && nEventsProfiling=2
+ [[ -z ${profilingCommand} ]] && profilingCommand="/usr/bin/valgrind --tool=callgrind --num-callers=40 -v --trace-children=yes"
+ submit "valgrind" 1 1 000 "${alirootEnv} ${self}" CPass0 ${commonOutputPath}/000${runNumber}/valgrind ${oneInputFile} ${nEventsProfiling} ${currentDefaultOCDB} ${configFile} ${runNumber} valgrind useProfilingCommand=${profilingCommand} "${extraOpts[@]}"
fi
################################################################################
echo "requested success rate is ${percentProcessedFilesToContinue}%"
echo "merging will start after ${nFilesToWaitFor} jobs are done"
- submit ${JOBID1} 1 ${nFiles} 000 "${alirootEnv} ${self}" "CPass0 ${targetDirectory} ${localInputList} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} -1 ${extraOpts}"
+ submit ${JOBID1} 1 ${nFiles} 000 "${alirootEnv} ${self}" CPass0 ${targetDirectory} ${localInputList} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} -1 "${extraOpts[@]}"
## submit a monitoring job that will run until a certain number of jobs are done with reconstruction
- submit "${JOBID1wait}" 1 1 000 "${alirootEnv} ${self}" "WaitForOutput ${commonOutputPath} 'meta/cpass0.job*.run${runNumber}.done' ${nFilesToWaitFor} ${maxSecondsToWait} '-maxdepth 1'"
+ submit "${JOBID1wait}" 1 1 000 "${alirootEnv} ${self}" WaitForOutput ${commonOutputPath} "meta/cpass0.job*.run${runNumber}.done" ${nFilesToWaitFor} ${maxSecondsToWait} '-maxdepth 1'
LASTJOB=${JOBID1wait}
fi #end running CPass0
[[ -f ${file} ]] && echo "copying ${file}" && cp -f ${file} ${commonOutputPath}
done
- submit ${JOBID2} 1 1 "${LASTJOB}" "${alirootEnv} ${self}" "MergeCPass0 ${targetDirectory} ${currentDefaultOCDB} ${configFile} ${runNumber} cpass0.calib.run${runNumber}.list ${extraOpts}"
+ submit ${JOBID2} 1 1 "${LASTJOB}" "${alirootEnv} ${self}" MergeCPass0 ${targetDirectory} ${currentDefaultOCDB} ${configFile} ${runNumber} cpass0.calib.run${runNumber}.list "${extraOpts[@]}"
LASTJOB=${JOBID2}
if [[ -n ${generateMC} ]]; then
- submit "mrl${JOBpostfix}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" "PrintValues sim ${commonOutputPath}/meta/sim.run${runNumber}.list ${commonOutputPath}/meta/cpass0.job*.run${runNumber}.done"
+ submit "mrl${JOBpostfix}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" PrintValues sim ${commonOutputPath}/meta/sim.run${runNumber}.list ${commonOutputPath}/meta/cpass0.job*.run${runNumber}.done
LASTJOB="mrl${JOBpostfix}"
fi
echo "requested success rate is ${percentProcessedFilesToContinue}%"
echo "merging will start after ${nFilesToWaitFor} jobs are done"
- submit ${JOBID4} 1 ${nFiles} "${LASTJOB}" "${alirootEnv} ${self}" "CPass1 ${targetDirectory} ${localInputList} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} -1 ${extraOpts}"
+ submit ${JOBID4} 1 ${nFiles} "${LASTJOB}" "${alirootEnv} ${self}" CPass1 ${targetDirectory} ${localInputList} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} -1 "${extraOpts[@]}"
################################################################################
## submit a monitoring job that will run until a certain number of jobs are done with reconstruction
- submit "${JOBID4wait}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" "WaitForOutput ${commonOutputPath} 'meta/cpass1.job*.run${runNumber}.done' ${nFilesToWaitFor} ${maxSecondsToWait} '-maxdepth 1'"
+ submit "${JOBID4wait}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" WaitForOutput ${commonOutputPath} "meta/cpass1.job*.run${runNumber}.done" ${nFilesToWaitFor} ${maxSecondsToWait} '-maxdepth 1'
LASTJOB=${JOBID4wait}
################################################################################
[[ -f ${file} ]] && echo "copying ${file}" && cp -f ${file} ${commonOutputPath}
done
- submit "${JOBID5}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" "MergeCPass1 ${targetDirectory} ${currentDefaultOCDB} ${configFile} ${runNumber} cpass0.calib.run${runNumber}.list cpass1.QA.run${runNumber}.lastMergingStage.txt.list ${extraOpts}"
+ submit "${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 "${extraOpts[@]}"
LASTJOB=${JOBID5}
echo
fi
- ##############################
- if [ ${runESDfiltering} -eq 1 ]; then
- rm -f ${commonOutputPath}/cpass1.ESD.run${runNumber}.list
- rm -f ${commonOutputPath}/meta/filtering.cpass1.run*.done
- echo
- echo submitting filtering for run ${runNumber}
- echo
- submit "${JOBmakeESDlistCPass1}" 1 1 "${LASTJOB}" "${self}" "PrintValues esd ${commonOutputPath}/meta/cpass1.ESD.run${runNumber}.list ${commonOutputPath}/meta/cpass1.job*.run${runNumber}.done "
- 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 ${extraOpts}"
- LASTJOB=${JOBfilterESDcpass1}
- fi
+ ###############################
+ #if [ ${runESDfiltering} -eq 1 ]; then
+ # rm -f ${commonOutputPath}/cpass1.ESD.run${runNumber}.list
+ # rm -f ${commonOutputPath}/meta/filtering.cpass1.run*.done
+ # echo
+ # echo submitting filtering for run ${runNumber}
+ # echo
+ # submit "${JOBmakeESDlistCPass1}" 1 1 "${LASTJOB}" "${self}" PrintValues esd ${commonOutputPath}/meta/cpass1.ESD.run${runNumber}.list ${commonOutputPath}/meta/cpass1.job*.run${runNumber}.done
+ # 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[@]}"
+ # LASTJOB=${JOBfilterESDcpass1}
+ #fi
done
#################################################################################
#################################################################################
- if [ ${runESDfiltering} -eq 1 ]; then
- submit "${JOBID5wait}" 1 1 "${LASTJOB}" "${self}" "WaitForOutput ${commonOutputPath} 'meta/filtering.cpass1.run*.done' ${#listOfRuns[@]} ${maxSecondsToWait}"
- else
- submit "${JOBID5wait}" 1 1 "${LASTJOB}" "${self}" "WaitForOutput ${commonOutputPath} 'meta/merge.cpass1.run*.done' ${#listOfRuns[@]} ${maxSecondsToWait}"
- fi
+ #if [ ${runESDfiltering} -eq 1 ]; then
+ # submit "${JOBID5wait}" 1 1 "${LASTJOB}" "${self}" WaitForOutput ${commonOutputPath} "meta/filtering.cpass1.run*.done" "${#listOfRuns[@]}" ${maxSecondsToWait}
+ #else
+ submit "${JOBID5wait}" 1 1 "${LASTJOB}" "${self}" WaitForOutput ${commonOutputPath} "meta/merge.cpass1.run*.done" ${#listOfRuns[@]} ${maxSecondsToWait}
+ #fi
LASTJOB=${JOBID5wait}
#################################################################################
echo "submit make a summary"
echo
- submit "${JOBID6}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" "MakeSummary ${configFile}"
+ submit "${JOBID6}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" MakeSummary ${configFile}
LASTJOB=${JOBID6}
#################################################################################
}
goWaitForOutput()
-{
+(
umask 0002
[[ $# -lt 3 ]] && echo "goWaitForOutput() wrong number of arguments, exiting.." && return 1
echo searchPath=${1}
done
echo "DONE! exiting..."
return 0
-}
+)
mergeSysLogs()
-{
+(
outputFile=${1}
shift
inputFiles="$@"
(( i++ ))
done < <(ls -1 ${inputFiles}) > ${outputFile}
return 0
-}
+)
goMakeMergedSummaryTree()
-{
+(
# create list of calibration entries
# takes no arguments, just run it in the base output
# directory with the following files in the working directory
# summary_pass0.tree
# summary_pass1.tree
#
-
+
[[ ! -f cpass0.dcsTree.list ]] && echo "no cpass0.dcsTree.list" && return 1
[[ ! -f cpass1.dcsTree.list ]] && echo "no cpass1.dcsTree.list" && return 1
[[ ! -f trending.root ]] && echo "no trending.root" && return 1
//
// Calibration values dump
//
+ //Printf("MakeTreeFromList cpass0.dcsTree.list");
AliXRDPROOFtoolkit::MakeTreeFromList("Calib.TPC.CPass0.root", "dcs","dcs","cpass0.dcsTree.list",1);
+ //Printf("MakeTreeFromList cpass1.dcsTree.list");
AliXRDPROOFtoolkit::MakeTreeFromList("Calib.TPC.CPass1.root", "dcs","dcs","cpass1.dcsTree.list",1);
//
// Calibration status dump
//
TFile *fprod = TFile::Open("fproduction.root","recreate");
TTree tree0, tree1;
+ //Printf("reading summary_pass0.tree");
tree0.ReadFile("summary_pass0.tree");
+ //Printf("reading summary_pass1.tree");
tree1.ReadFile("summary_pass1.tree");
tree0.Write("CPass0");
tree1.Write("CPass1");
stringSetup+="1#CPass0#runnumber#CPass0#fproduction.root+"; //
stringSetup+="1#CPass1#runnumber#CPass1#fproduction.root+"; //
//
+ //Printf("stringSetup: %s", stringSetup.Data());
AliXRDPROOFtoolkit::JoinTreesIndex("outAll.root","joinAll","run",stringSetup.Data(), 1);
}
EOF
aliroot -b -q "mergeTree.C" > mergeTrees.log
return $?
-}
+)
goMakeSummary()
-{
+(
#all the final stuff goes in here for ease of use:
# summary logs
# qa plot making
# final file lists
+ #some defaults:
+ log="summary.log"
+ productionID="qa"
configFile=${1}
shift 1
- extraOpts="$@"
- log="summary.log"
- productionID="qa"
- parseConfig ${configFile} ${extraOpts}
+ extraOpts=("$@")
+ if ! parseConfig ${configFile} "${extraOpts[@]}"; then return 1; fi
+
+ #if which greadlink; then configFile=$(greadlink -f ${configFile}); fi
+
+ #record the working directory provided by the batch system
+ batchWorkingDirectory=${PWD}
[[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
- exec &> >(tee ${log})
-
[[ ! -f ${configFile} ]] && echo "no config file ${configFile}!" && return
[[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
+ #copy some useful stuff
+ #and go to the commonOutputPath
+ cp ${configFile} ${commonOutputPath}
+ cd ${commonOutputPath}
+
+ exec &> >(tee ${log})
+
#summarize the global stuff
echo "env script: ${alirootSource} ${alirootEnv}"
echo "\$ALICE_ROOT=${ALICE_ROOT}"
rm -f trending.list
goPrintValues trendingfile trending.list ${commonOutputPath}/meta/merge.cpass1.run*.done &>/dev/null
rm -f filtering.list
- goPrintValues filteredTree filtering.list ${commonOutputPath}/meta/filtering.cpass1.run*.done &>/dev/null
- #/bin/ls ${commonOutputPath}/*/cpass0/dcs* > cpass0.dcsTree.list
+ goPrintValues filteredTree filtering.list ${commonOutputPath}/meta/merge.cpass1.run*.done &>/dev/null
rm -f cpass0.dcsTree.list
goPrintValues dcsTree cpass0.dcsTree.list ${commonOutputPath}/meta/merge.cpass0.run*.done &>/dev/null
- #/bin/ls ${commonOutputPath}/*/cpass1/dcs* > cpass1.dcsTree.list
rm -f cpass1.dcsTree.list
goPrintValues dcsTree cpass1.dcsTree.list ${commonOutputPath}/meta/merge.cpass1.run*.done &>/dev/null
#merge trending
rm -f ${commonOutputPath}/trending_merged.root
- goMerge trending.list ${commonOutputPath}/trending.root ${configFile} ${extraOpts} &> mergeTrending.log
+ goMerge trending.list ${commonOutputPath}/trending.root ${configFile} "${extraOpts[@]}" &> mergeTrending.log
goMakeSummaryTree ${commonOutputPath} 0
goMakeSummaryTree ${commonOutputPath} 1
- goCreateQAplots qa.list ${productionID} QAplots ${configFile} ${extraOpts} &>createQAplots.log
+ goCreateQAplots "${PWD}/qa.list" "${productionID}" "QAplots" "${configFile}" "${extraOpts[@]}" filteringList="${PWD}/filtering.list" &>createQAplots.log
#make a merged summary tree out of the QA trending, dcs trees and log summary trees
goMakeMergedSummaryTree
[[ -n ${MAILTO} ]] && cat ${log} | mail -s "benchmark ${productionID} done" ${MAILTO}
return 0
-}
+)
goMakeSummaryTree()
-{
+(
if [[ $# -lt 1 ]] ; then
return
fi
done
return 0
-}
+)
parseConfig()
{
configFile=${1}
shift
+ args=("$@")
+
+
+ #some defaults
+ #autoOCDB=0
+ defaultOCDB="raw://"
+ #runNumber=167123
+ #makeflowPath="/hera/alice/aux/cctools/bin"
+ #makeflowOptions="-T wq -N alice -d all -C ali-copilot.cern.ch:9097"
+ #makeflowOptions="-T wq -N alice -C ali-copilot.cern.ch:9097"
+ makeflowOptions=""
+ #batchCommand="/usr/bin/qsub"
+ batchFlags="-b y -cwd -l h_rt=24:0:0,h_rss=4G "
+ baseOutputDirectory="$PWD/output"
+ #alirootEnv="/cvmfs/alice.cern.ch/bin/alienv setenv AliRoot/v5-04-34-AN -c"
+ #alirootEnv="/home/mkrzewic/alisoft/balice_master.sh"
+ #trustedQAtrainMacro='/hera/alice/mkrzewic/gsisvn/Calibration/QAtrain_duo.C'
+ reconstructInTemporaryDir=0
+ recoTriggerOptions="\"\""
+ percentProcessedFilesToContinue=100
+ maxSecondsToWait=$(( 3600*24 ))
+ nEvents=-1
+ nMaxChunks=0
+ postSetUpActionCPass0=""
+ postSetUpActionCPass1=""
+ runCPass0reco=1
+ runCPass0MergeMakeOCDB=1
+ runCPass1reco=1
+ runCPass1MergeMakeOCDB=1
+ runESDfiltering=1
+ filteringFactorHighPt=1e2
+ filteringFactorV0s=1e1
+ MAILTO=""
+ #pretend=1
+ #dontRedirectStdOutToLog=1
+ logToFinalDestination=1
+ ALIROOT_FORCE_COREDUMP=1
+ pretendDelay=0
#first, source the config file
if [ -f ${configFile} ]; then
source ${configFile}
else
- echo "config file ${configFile} not found!, skipping..."
+ echo "config file ${configFile} not found!"
+ return 1
fi
- #then, parse the options as theya override the optionf from file
- while [[ -n ${1} ]]; do
- var="${1#--}"
- echo "extraOpts: exporting ${var}"
- eval "export ${var}"
- shift
+ unset encodedSpaces
+ for opt in "${args[@]}"; do
+ [[ "${opt}" =~ encodedSpaces=.* ]] && encodedSpaces=1 && echo "encodedSpaces!" && break
done
+ #then, parse the options as they override the options from file
+ for opt in "${args[@]}"; do
+ [[ -z ${opt} ]] && continue
+ [[ -n ${encodedSpaces} ]] && opt="$(decSpaces ${opt})"
+ [[ "${opt}" =~ ^[[:space:]]*$ ]] && continue
+ if [[ ! "${opt}" =~ .*=.* ]]; then
+ echo "badly formatted option \"${opt}\" should be: option=value, stopping..."
+ return 1
+ fi
+ local var="${opt%%=*}"
+ local value="${opt#*=}"
+ echo "${var} = ${value}"
+ export ${var}="${value}"
+ done
+
+ #do some checking
+ [[ -z ${alirootEnv} ]] && echo "alirootEnv not defined!" && return 1
+
#export the aliroot function if defined to override normal behaviour
[[ $(type -t aliroot) =~ "function" ]] && export -f aliroot
+
return 0
}
aliroot()
{
args="$@"
- if [[ -n ${valgrindCommand} ]]; then
+ if [[ -n ${useProfilingCommand} ]]; then
valgrindLogFile="cpu.txt"
[[ "${args}" =~ rec ]] && valgrindLogFile="cpu_rec.txt"
[[ "${args}}" =~ Calib ]] && valgrindLogFile="cpu_calib.txt"
- [[ -n ${valgrindCommand} ]] && valgrindCommand="${valgrindCommand} --log-file=${valgrindLogFile}"
- echo running ${valgrindCommand} aliroot ${args}
- ${valgrindCommand} aliroot ${args}
+ [[ -n ${useProfilingCommand} ]] && useProfilingCommand="${useProfilingCommand} --log-file=${valgrindLogFile}"
+ echo running ${useProfilingCommand} aliroot ${args}
+ ${useProfilingCommand} aliroot ${args}
else
#to prevent an infinite recursion use "command aliroot" to disable
#aliases and functions
echo running command aliroot ${args}
- command aliroot ${args}
+ command aliroot "$@"
fi
return 0
}
return 0
}
+#these functions encode strings to and from a space-less form
+#use when spaces are not well handled (e.g. in arguments to
+#commands in makeflow files, etc.
+encSpaces()(echo "${1// /@@@@}")
+decSpaces()(echo "${1//@@@@/ }")
+
main "$@"
git://git.uio.no / u / mrichter / AliRoot.git / blobdiff