#!/bin/bash
#include benchmark.config
+# blame: Mikolaj Krzewicki, mkrzewic@cern.ch
# this script runs the CPass0/CPass1 train
# produced OCDB updates are local
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}
if [[ -z ${jobindex} || ${jobindex} -lt 0 ]]; then
[[ -n "${LSB_JOBINDEX}" ]] && jobindex=${LSB_JOBINDEX}
[[ -n "${SGE_TASK_ID}" ]] && jobindex=${SGE_TASK_ID}
+ if [[ -z ${jobindex} ]]; then
+ echo "no jobindex!"
+ return 1
+ fi
fi
[[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
- doneFile="${commonOutputPath}/meta/cpass0.job${jobindex}.run${runNumber}.done"
+
+ # This file signals that/if everything went fine
+ doneFileBase="cpass0.job${jobindex}.run${runNumber}.done"
+ [[ -n ${useProfilingCommand} ]] && doneFileBase="profiling.cpass0.job${jobindex}.run${runNumber}.done"
+
+ # We will have two copies of the file
+ mkdir -p "${commonOutputPath}/meta" || return 1
+ doneFileTmp="${batchWorkingDirectory}/${doneFileBase}"
+ doneFile="${commonOutputPath}/meta/${doneFileBase}"
[[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
outputDir=${targetDirectory}/${jobindex}_${chunkName%.*}
mkdir -p ${outputDir}
- [[ ! -d ${outputDir} ]] && echo "cannot make ${outputDir}" && touch ${doneFile} && return 1
+ if [[ ! -d ${outputDir} ]]; then
+ touch ${doneFileTmp}
+ echo "cannot make ${outputDir}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
- #runpath=${PWD}/rundir_cpass0_${runNumber}_${jobindex}
runpath=${outputDir}
- [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
- [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
+ [[ ${reconstructInTemporaryDir} -eq 1 ]] && runpath=$(mktemp -d -t cpass0.XXXXXX)
+ [[ ${reconstructInTemporaryDir} -eq 2 ]] && runpath=${PWD}/rundir_cpass0_${runNumber}_${jobindex}
mkdir -p ${runpath}
- [[ ! -d ${runpath} ]] && echo "cannot make runpath ${runpath}" && touch ${doneFile} && return 1
- cd ${runpath}
- [[ ! ${PWD} =~ ${runpath} ]] && echo "PWD=$PWD is not the runpath=${runpath}" && touch ${doneFile} && return 1
+ if [[ ! -d ${runpath} ]]; then
+ touch ${doneFileTmp}
+ echo "cannot make runpath ${runpath}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
+ if ! cd ${runpath}; then
+ touch ${doneFileTmp}
+ echo "PWD=$PWD is not the runpath=${runpath}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
#runCPassX/C expects the raw chunk to be linked in the run dir
#despite it being accessed by the full path
- ln -s ${infile} ${runpath}/${chunkName}
+ if [[ $copyInputData == 0 ]]; then
+ ln -s ${infile} ${runpath}/${chunkName}
+ else
+ copyFileToLocal ${infile} ${runpath}/${chunkName}
+ fi
#####MC
if [[ -n ${generateMC} ]]; then
olddir=${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 ${simrunpath}
-
- filesMC=(
- "${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
+ 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
######
- [[ ! -f ${inputList} && -z ${pretend} ]] && echo "input file ${inputList} not found, exiting..." && touch ${doneFile} && return 1
+ if [[ "${inputList}" == "${inputList%%://*}" && ! -f "${inputList}" && -z ${pretend} ]]; then
+ touch ${doneFileTmp}
+ echo "input file ${inputList} not found, exiting..." >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
logOutputDir=${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 "#####################"
echo CPass0:
echo JOB setup
- echo nEvents ${nEvents}
- echo runNumber ${runNumber}
- echo ocdbPath ${ocdbPath}
- echo infile ${infile}
- echo chunkName ${chunkName}
- echo jobindex ${jobindex}
- echo recoTriggerOptions ${recoTriggerOptions}
- echo targetDirectory ${targetDirectory}
- echo commonOutputPath ${commonOutputPath}
- echo doneFile ${doneFile}
- echo runpath ${runpath}
- echo outputDir ${outputDir}
- echo ALICE_ROOT ${ALICE_ROOT}
- echo PWD ${PWD}
+ echo nEvents ${nEvents}
+ echo runNumber ${runNumber}
+ echo ocdbPath ${ocdbPath}
+ echo infile ${infile}
+ echo chunkName ${chunkName}
+ echo jobindex ${jobindex}
+ echo recoTriggerOptions ${recoTriggerOptions}
+ echo targetDirectory ${targetDirectory}
+ echo commonOutputPath ${commonOutputPath}
+ echo doneFile ${doneFile}
+ echo batchWorkingDirectory ${batchWorkingDirectory}
+ echo runpath ${runpath}
+ echo outputDir ${outputDir}
+ echo PWD ${PWD}
+ echo ALICE_ROOT ${ALICE_ROOT}
echo "########## ###########"
alirootInfo > ALICE_ROOT.log
fi
#run CPass0
- echo "${runpath}/runCPass0.sh ${infile} ${nEvents} ${runNumber} ${ocdbPath} ${recoTriggerOptions}"
+ echo "${runpath}/runCPass0.sh /${infile} ${nEvents} ${runNumber} ${ocdbPath} ${recoTriggerOptions}"
if [[ -n ${pretend} ]]; then
+ sleep ${pretendDelay}
touch AliESDs.root
touch AliESDfriends.root
touch AliESDfriends_v1.root
touch rec.log
touch calib.log
else
- echo ./runCPass0.sh "${infile}" "${nEvents}" "${runNumber}" "${ocdbPath}" "${recoTriggerOptions}"
- ./runCPass0.sh "${infile}" "${nEvents}" "${runNumber}" "${ocdbPath}" "${recoTriggerOptions}"
+ #caveat: in the local case, first arg must start with a slash
+ ./runCPass0.sh "/${infile}" "${nEvents}" "${runNumber}" "${ocdbPath}" "${recoTriggerOptions}"
fi
#move stuff to final destination
/bin/ls
echo
+ # [dberzano] OK this is fine!
echo rm -f ./${chunkName}
rm -f ./${chunkName}
- echo "cp --recursive ${runpath}/* ${outputDir}"
- cp -p --recursive ${runpath}/* ${outputDir}
+ echo "paranoidCp ${runpath}/* ${outputDir}"
+ paranoidCp ${runpath}/* ${outputDir}
echo
#validate CPass0
cd ${outputDir}
- touch ${doneFile}
- echo "dir ${outputDir}" >> ${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}
+ if summarizeLogs >> ${doneFileTmp}; then
+ [[ -f ${outputDirMC}/galice.root ]] && echo "sim ${outputDirMC}/galice.root" >> ${doneFileTmp}
+ [[ -f AliESDfriends_v1.root ]] && echo "calibfile ${outputDir}/AliESDfriends_v1.root" >> ${doneFileTmp}
+ [[ -f AliESDs.root ]] && echo "esd ${outputDir}/AliESDs.root" >> ${doneFileTmp}
fi
- [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
+ [[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath} && echo "removing ${runpath}"
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
return 0
-}
+)
goCPass1()
-{
+(
umask 0002
targetDirectory=${1}
if [[ -z ${jobindex} || ${jobindex} -lt 0 ]]; then
[[ -n "${LSB_JOBINDEX}" ]] && jobindex=${LSB_JOBINDEX}
[[ -n "${SGE_TASK_ID}" ]] && jobindex=${SGE_TASK_ID}
+ if [[ -z ${jobindex} ]]; then
+ echo "no jobindex!"
+ return 1
+ fi
fi
[[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
- doneFile="${commonOutputPath}/meta/cpass1.job${jobindex}.run${runNumber}.done"
+
+ # This file signals that/if everything went fine
+ doneFileBase="cpass1.job${jobindex}.run${runNumber}.done"
+ [[ -n ${useProfilingCommand} ]] && doneFileBase="profiling.cpass0.job${jobindex}.run${runNumber}.done"
+
+ # We will have two copies of the file
+ mkdir -p "${commonOutputPath}/meta" || return 1
+ doneFileTmp="${batchWorkingDirectory}/${doneFileBase}"
+ doneFile="${commonOutputPath}/meta/${doneFileBase}"
[[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
#Packages= ;OutputDir= ;LPMPass= ;TriggerAlias= ;LPMRunNumber= ;LPMProductionType= ;LPMInteractionType= ;LPMProductionTag= ;LPMAnchorRun= ;LPMAnchorProduction= ;LPMAnchorYear=
export PRODUCTION_METADATA="OutputDir=cpass1"
- [[ ! -f ${inputList} && -z ${pretend} ]] && echo "input file ${inputList} not found, exiting..." && touch ${doneFile} && return 1
+ if [[ "${inputList}" == "${inputList%%://*}" && ! -f "${inputList}" && -z ${pretend} ]]; then
+ touch ${doneFileTmp}
+ echo "input file ${inputList} not found, exiting..." >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
if [[ "${inputList}" =~ \.root$ ]]; then
infile=${inputList}
else
outputDir=${targetDirectory}/${jobindex}_${chunkName%.*}
mkdir -p ${outputDir}
- [[ ! -d ${outputDir} ]] && echo "cannot make ${outputDir}" && touch ${doneFile} && return 1
+ if [[ ! -d ${outputDir} ]];then
+ touch ${doneFileTmp}
+ echo "cannot make ${outputDir}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
- #runpath=${PWD}/rundir_cpass1_${runNumber}_${jobindex}
runpath=${outputDir}
- [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
- [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
+ [[ ${reconstructInTemporaryDir} -eq 1 ]] && runpath=$(mktemp -d -t cpass1.XXXXXX)
+ [[ ${reconstructInTemporaryDir} -eq 2 ]] && runpath=${PWD}/rundir_cpass1_${runNumber}_${jobindex}
#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}
- [[ ! ${PWD} =~ ${runpath} ]] && echo "PWD=$PWD is not the runpath=${runpath}" && touch ${doneFile} && return 1
+ if [[ ! -d ${runpath} ]]; then
+ touch ${doneFileTmp}
+ echo "cannot make runpath ${runpath}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
+ if ! cd ${runpath}; then
+ touch ${doneFileTmp}
+ echo "PWD=$PWD is not the runpath=${runpath}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
#this is needed for runCPass1.sh
- ln -s ${infile} ${runpath}/${chunkName}
+ if [[ $copyInputData == 0 ]]; then
+ ln -s ${infile} ${runpath}/${chunkName}
+ else
+ copyFileToLocal ${infile} ${runpath}/${chunkName}
+ 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 "#####################"
echo CPass1:
echo JOB setup
- echo nEvents ${nEvents}
- echo runNumber ${runNumber}
- echo ocdbPath ${ocdbPath}
- echo infile ${infile}
- echo chunkName ${chunkName}
- echo jobindex ${jobindex}
- echo recoTriggerOptions ${recoTriggerOptions}
- echo targetDirectory ${targetDirectory}
- echo commonOutputPath ${commonOutputPath}
- echo doneFile ${doneFile}
- echo runpath ${runpath}
- echo outputDir ${outputDir}
- echo ALICE_ROOT ${ALICE_ROOT}
- echo PWD ${PWD}
- echo "########## ###########"
+ echo nEvents ${nEvents}
+ echo runNumber ${runNumber}
+ echo ocdbPath ${ocdbPath}
+ echo infile ${infile}
+ echo chunkName ${chunkName}
+ echo jobindex ${jobindex}
+ echo recoTriggerOptions ${recoTriggerOptions}
+ echo targetDirectory ${targetDirectory}
+ echo commonOutputPath ${commonOutputPath}
+ echo doneFile ${doneFile}
+ echo runpath ${runpath}
+ echo outputDir ${outputDir}
+ echo batchWorkingDirectory ${batchWorkingDirectory}
+ echo ALICE_ROOT ${ALICE_ROOT}
+ echo PWD ${PWD}
+ echo "#####################"
alirootInfo > ALICE_ROOT.log
"${batchWorkingDirectory}/runCalibTrain.C"
"${batchWorkingDirectory}/QAtrain_duo.C"
"${batchWorkingDirectory}/localOCDBaccessConfig.C"
+ "${batchWorkingDirectory}/${configFile}"
"${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz"
"${batchWorkingDirectory}/OCDB.root"
"${trustedQAtrainMacro}"
"${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 ]] && chmod +x ${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
fi
if [[ ! $(/bin/ls -1 OCDB/*/*/*/*.root 2>/dev/null) ]]; then
- echo "cpass0 produced no calibration! exiting..."
- touch ${doneFile}
+ touch ${doneFileTmp}
+ echo "cpass0 produced no calibration! exiting..." >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
return 1
fi
#create the Barrel and OuterDet directories for CPass1 and link the local OCDB directory
#there to make the localOCDBaccessConfig.C file work, since it may point to the OCDB
#entries using a relative path, e.g. local://./OCDB
+ echo "linking the OCDB/ for Barrel and OuterDet directories"
mkdir Barrel OuterDet
+ ls -l
ln -s ../OCDB Barrel/OCDB
ln -s ../OCDB OuterDet/OCDB
#run CPass1
chmod u+x runCPass1.sh
- echo "${runpath}/runCPass1.sh ${infile} ${nEvents} ${runNumber} ${ocdbPath} ${recoTriggerOptions}"
+ echo "${runpath}/runCPass1.sh /${infile} ${nEvents} ${runNumber} ${ocdbPath} ${recoTriggerOptions}"
if [[ -n ${pretend} ]]; then
+ sleep ${pretendDelay}
touch AliESDs_Barrel.root
touch AliESDfriends_Barrel.root
touch AliESDfriends_v1.root
touch qa.log
touch filtering.log FilterEvents_Trees.root
else
- ./runCPass1.sh "${infile}" "${nEvents}" "${runNumber}" "${ocdbPath}" "${recoTriggerOptions}"
+ #caveat: in the local case, first arg must start with a slash
+ ./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
#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 ]]; then
- goMakeFilteredTrees ${PWD} ${runNumber} "filtered.list" ${filteringFactorHighPt} ${filteringFactorV0s} ${ocdbPath} 1000000 0 10000000 0 ${configFile} AliESDs_Barrel.root "${extraOpts[@]}" >filtering.log
+ 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
/bin/ls
echo rm -f ./${chunkName}
rm -f ./${chunkName}
- echo "cp --recursive ${runpath}/* ${outputDir}"
- cp -pf --recursive ${runpath}/* ${outputDir}
+ echo "paranoidCp ${runpath}/* ${outputDir}"
+ paranoidCp ${runpath}/* ${outputDir}
echo
#validate CPass1
cd ${outputDir}
- touch ${doneFile}
- echo "dir ${outputDir}" >> ${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}
+ if summarizeLogs >> ${doneFileTmp}; then
+ [[ -f AliESDs_Barrel.root ]] && echo "esd ${outputDir}/AliESDs_Barrel.root" >> ${doneFileTmp}
+ [[ -f AliESDfriends_v1.root ]] && echo "calibfile ${outputDir}/AliESDfriends_v1.root" >> ${doneFileTmp}
+ [[ -f QAresults_Barrel.root ]] && echo "qafile ${outputDir}/QAresults_Barrel.root" >> ${doneFileTmp}
+ [[ -f QAresults_Outer.root ]] && echo "qafile ${outputDir}/QAresults_Outer.root" >> ${doneFileTmp}
+ [[ -f QAresults_barrel.root ]] && echo "qafile ${outputDir}/QAresults_barrel.root" >> ${doneFileTmp}
+ [[ -f QAresults_outer.root ]] && echo "qafile ${outputDir}/QAresults_outer.root" >> ${doneFileTmp}
+ [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFileTmp}
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}
+ if grep "qa_outer.log.*OK" ${doneFileTmp} > /dev/null; then
+ [[ -f QAresults_Outer.root ]] && echo "qafile ${outputDir}/QAresults_Outer.root" >> ${doneFileTmp}
+ [[ -f QAresults_outer.root ]] && echo "qafile ${outputDir}/QAresults_outer.root" >> ${doneFileTmp}
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}
+ if grep "qa_barrel.log.*OK" ${doneFileTmp} > /dev/null; then
+ [[ -f QAresults_Barrel.root ]] && echo "qafile ${outputDir}/QAresults_Barrel.root" >> ${doneFileTmp}
+ [[ -f QAresults_barrel.root ]] && echo "qafile ${outputDir}/QAresults_barrel.root" >> ${doneFileTmp}
fi
- if grep "filtering.log.*OK" ${doneFile} > /dev/null; then
- [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
+ if grep "filtering.log.*OK" ${doneFileTmp} > /dev/null; then
+ [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFileTmp}
fi
fi
[[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
return 0
-}
+)
goMergeCPass0()
-{
+(
#
# find the output files and merge them
#
batchWorkingDirectory=${PWD}
[[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
- doneFile="${commonOutputPath}/meta/merge.cpass0.run${runNumber}.done"
+
+ # This file signals that everything went fine
+ doneFileBase="merge.cpass0.run${runNumber}.done"
+
+ # We will have two copies of the file
+ mkdir -p "${commonOutputPath}/meta" || return 1
+ doneFileTmp="${batchWorkingDirectory}/${doneFileBase}"
+ doneFile="${commonOutputPath}/meta/${doneFileBase}"
umask 0002
ulimit -c unlimited
[[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
- #runpath=${PWD}/rundir_cpass0_Merge_${runNumber}
runpath=${outputDir}
- [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
- [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
+ [[ ${reconstructInTemporaryDir} -eq 1 ]] && runpath=$(mktemp -d -t mergeCPass0.XXXXXX)
+ [[ ${reconstructInTemporaryDir} -eq 2 ]] && runpath=${PWD}/rundir_mergeCPass0_${runNumber}
mkdir -p ${runpath}
- [[ ! -d ${runpath} ]] && echo "not able to make the runpath ${runpath}" && touch ${doneFile} && return 1
- cd ${runpath}
- [[ ! ${PWD} =~ ${runpath} ]] && echo "PWD=$PWD is not the runpath=${runpath}" && touch ${doneFile} && return 1
+ if [[ ! -d ${runpath} ]]; then
+ touch ${doneFileTmp}
+ echo "not able to make the runpath ${runpath}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
+ if ! cd ${runpath}; then
+ touch ${doneFileTmp}
+ echo "PWD=$PWD is not the runpath=${runpath}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
logOutputDir=${runpath}
[[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
- [[ -z ${dontRedirectStdOutToLog} ]] && exec &> ${logOutputDir}/mergeMakeOCDB.log
+ [[ -z ${dontRedirectStdOutToLog} ]] && exec &> ${logOutputDir}/stdout
echo "${0} $*"
mergingScript="mergeMakeOCDB.byComponent.sh"
/bin/ls -1 ${outputDir}/*/AliESDfriends_v1.root 2>/dev/null > ${calibrationFilesToMerge}
fi
- echo "${mergingScript} ${calibrationFilesToMerge} ${runNumber} local://./OCDB ${ocdbStorage}"
+ echo "${mergingScript} ${calibrationFilesToMerge} ${runNumber} local://./OCDB defaultOCDB=${ocdbStorage} fileAccessMethod=nocopy"
if [[ -n ${pretend} ]]; then
+ sleep ${pretendDelay}
touch CalibObjects.root
touch ocdb.log
touch merge.log
touch dcsTime.root
mkdir -p ./OCDB/TPC/Calib/TimeGain/
mkdir -p ./OCDB/TPC/Calib/TimeDrift/
- touch ./OCDB/TPC/Calib/TimeGain/someCalibObject_0-999999_cpass0.root
- touch ./OCDB/TPC/Calib/TimeDrift/otherCalibObject_0-999999_cpass0.root
+ echo "some calibration" >> ./OCDB/TPC/Calib/TimeGain/someCalibObject_0-999999_cpass0.root
+ echo "some calibration" >> ./OCDB/TPC/Calib/TimeDrift/otherCalibObject_0-999999_cpass0.root
else
- ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" ${ocdbStorage}
+ ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" defaultOCDB=${ocdbStorage} fileAccessMethod=nocopy >> "mergeMakeOCDB.log"
#produce the calib trees for expert QA (dcsTime.root)
goMakeLocalOCDBaccessConfig ./OCDB
### produce the output
#tar the produced OCDB for reuse
- tar czf ${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz ./OCDB
+ #tar czf ${commonOutputPath}/meta/cpass0.localOCDB.${runNumber}.tgz ./OCDB
+
+ # Create tarball with OCDB, store on the shared directory, create signal file on batch directory
+ mkdir -p ${commonOutputPath}/meta
+ baseTar="cpass0.localOCDB.${runNumber}.tgz"
+ tar czf ${batchWorkingDirectory}/${baseTar} ./OCDB && \
+ mv ${batchWorkingDirectory}/${baseTar} ${commonOutputPath}/meta/${baseTar} && \
+ touch ${batchWorkingDirectory}/${baseTar}.done
/bin/ls
#copy all to output dir
- cp -pf --recursive ${runpath}/* ${outputDir}
+ echo "paranoidCp ${runpath}/* ${outputDir}"
+ paranoidCp ${runpath}/* ${outputDir}
if [[ -n ${generateMC} ]]; then
goPrintValues sim ${commonOutputPath}/meta/sim.run${runNumber}.list ${commonOutputPath}/meta/cpass0.job*.run${runNumber}.done
#validate merging cpass0
cd ${outputDir}
- touch ${doneFile}
- echo "dir ${outputDir}" >> ${doneFile}
- if summarizeLogs >> ${doneFile}; then
- [[ -f CalibObjects.root ]] && echo "calibfile ${outputDir}/CalibObjects.root" >> ${doneFile}
- [[ -f dcsTime.root ]] && echo "dcsTree ${outputDir}/dcsTime.root" >> ${doneFile}
+ if summarizeLogs >> ${doneFileTmp}; then
+ [[ -f CalibObjects.root ]] && echo "calibfile ${outputDir}/CalibObjects.root" >> ${doneFileTmp}
+ [[ -f dcsTime.root ]] && echo "dcsTree ${outputDir}/dcsTime.root" >> ${doneFileTmp}
fi
[[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
return 0
-}
+)
goMergeCPass1()
-{
+(
#
# find the output files and merge them
#
batchWorkingDirectory=${PWD}
[[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
- doneFile="${commonOutputPath}/meta/merge.cpass1.run${runNumber}.done"
+
+ # This file signals that everything went fine
+ doneFileBase="merge.cpass1.run${runNumber}.done"
+
+ # We will have two copies of the file
+ mkdir -p "${commonOutputPath}/meta" || return 1
+ doneFileTmp="${batchWorkingDirectory}/${doneFileBase}"
+ doneFile="${commonOutputPath}/meta/${doneFileBase}"
umask 0002
ulimit -c unlimited
[[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
- #runpath=${PWD}/rundir_cpass1_Merge_${runNumber}
runpath=${outputDir}
- [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
- [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
+ [[ ${reconstructInTemporaryDir} -eq 1 ]] && runpath=$(mktemp -d -t mergeCPass1.XXXXXX)
+ [[ ${reconstructInTemporaryDir} -eq 2 ]] && runpath=${PWD}/rundir_mergeCPass1_${runNumber}
mkdir -p ${runpath}
- [[ ! -d ${runpath} ]] && echo "not able to make the runpath ${runpath}" && touch ${doneFile} && return 1
- cd ${runpath}
- [[ ! ${PWD} =~ ${runpath} ]] && echo "PWD=$PWD is not the runpath=${runpath}" && touch ${doneFile} && return 1
+ if [[ ! -d ${runpath} ]]; then
+ touch ${doneFileTmp}
+ echo "not able to make the runpath ${runpath}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
+ if ! cd ${runpath}; then
+ touch ${doneFileTmp}
+ echo "PWD=$PWD is not the runpath=${runpath}" >> ${doneFileTmp}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+ return 1
+ fi
logOutputDir=${runpath}
[[ -n ${logToFinalDestination} ]] && logOutputDir=${outputDir}
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 > ${qaFilesToMerge}
fi
-
- echo "${mergingScript} ${calibrationFilesToMerge} ${runNumber} local://./OCDB ${ocdbStorage}"
+
+ echo "${mergingScript} ${calibrationFilesToMerge} ${runNumber} local://./OCDB defaultOCDB=${ocdbStorage} fileAccessMethod=nocopy"
if [[ -n ${pretend} ]]; then
+ sleep ${pretendDelay}
touch ocdb.log
touch cpass1.localOCDB.${runNumber}.tgz
touch ${qaMergedOutputFileName}
touch ${qaMergedOutputFileName}
mkdir -p OCDB
else
- ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" ${ocdbStorage}
+ ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" defaultOCDB=${ocdbStorage} fileAccessMethod=nocopy
#merge QA (and filtered trees)
[[ -n ${AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF} ]] && export AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF
aliroot -b -q "${ALICE_ROOT}/PWGPP/TPC/macros/CalibSummary.C(${runNumber},\"${ocdbStorage}\")" > calibTree.log
fi
- tar czf ${commonOutputPath}/meta/cpass1.localOCDB.${runNumber}.tgz ./OCDB
+ # Create tarball with OCDB, store on the shared directory, create signal file on batch directory
+ mkdir -p ${commonOutputPath}/meta
+ baseTar="cpass1.localOCDB.${runNumber}.tgz"
+ tar czf ${batchWorkingDirectory}/${baseTar} ./OCDB && \
+ mv ${batchWorkingDirectory}/${baseTar} ${commonOutputPath}/meta/${baseTar} && \
+ touch ${batchWorkingDirectory}/${baseTar}.done
/bin/ls
#copy all to output dir
- cp -pf --recursive ${runpath}/* ${outputDir}
+ echo "paranoidCp ${runpath}/* ${outputDir}"
+ paranoidCp ${runpath}/* ${outputDir}
#validate merge cpass1
cd ${outputDir}
- touch ${doneFile}
- echo "dir ${outputDir}" >> ${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}
+ if summarizeLogs >> ${doneFileTmp}; then
+ [[ -f CalibObjects.root ]] && echo "calibfile ${outputDir}/CalibObjects.root" >> ${doneFileTmp}
+ [[ -f ${qaMergedOutputFileName} ]] && echo "qafile ${outputDir}/${qaMergedOutputFileName}" >> ${doneFileTmp}
+ [[ -f trending.root ]] && echo "trendingfile ${outputDir}/trending.root" >> ${doneFileTmp}
+ [[ -f dcsTime.root ]] && echo "dcsTree ${outputDir}/dcsTime.root" >> ${doneFileTmp}
+ [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFileTmp}
else
- if grep "mergeQA.log.*OK" ${doneFile} > /dev/null; then
- [[ -f ${qaMergedOutputFileName} ]] && echo "qafile ${outputDir}/${qaMergedOutputFileName}" >> ${doneFile}
+ if grep "mergeQA.log.*OK" ${doneFileTmp} > /dev/null; then
+ [[ -f ${qaMergedOutputFileName} ]] && echo "qafile ${outputDir}/${qaMergedOutputFileName}" >> ${doneFileTmp}
fi
- if grep "mergeFilteredTrees.log.*OK" ${doneFile} > /dev/null; then
- [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFile}
+ if grep "mergeFilteredTrees.log.*OK" ${doneFileTmp} > /dev/null; then
+ [[ -f FilterEvents_Trees.root ]] && echo "filteredTree ${outputDir}/FilterEvents_Trees.root" >> ${doneFileTmp}
fi
fi
[[ "${runpath}" != "${outputDir}" ]] && rm -rf ${runpath}
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
return 0
-}
+)
goMerge()
-{
+(
#generic root merge using CPass1 merge.C script
inputList=${1}
outputFile=${2}
- configFile=${3-"becnhmark.config"}
+ configFile=${3-"benchmark.config"}
shift 3
if ! parseConfig ${configFile} "$@"; then return 1; fi
rm -f ${outputFile}
aliroot -b -q "${ALICE_ROOT}/PWGPP/CalibMacros/CPass0/merge.C(\"${inputList}\",\"\",kFALSE,\"${outputFile}\")" > merge_${inputList}.log
return 0
-}
+)
goSubmitMakeflow()
{
commonOutputPath=${baseOutputDirectory}/${productionID}
if [[ -d ${commonOutputPath} ]]; then
echo "output dir ${commonOutputPath} exists!"
- return 1
+ #return 1
else
mkdir -p ${commonOutputPath}
fi
mkdir -p ${commonOutputPath}/meta
- self=$(readlink -f "${0}")
+ self=${0}
+ #if which greadlink; then self=$(greadlink -f "${0}"); fi
- cp ${self} ${commonOutputPath}
- cp ${configFile} ${commonOutputPath}
- cp ${inputList} ${commonOutputPath}
+ #for reference copy the setup to the output dir
+ paranoidCp ${self} ${commonOutputPath}
+ paranoidCp ${configFile} ${commonOutputPath}
+ paranoidCp ${inputFileList} ${commonOutputPath}
#submit - use makeflow if available, fall back to old stuff when makeflow not there
if which makeflow; then
-
goGenerateMakeflow ${productionID} ${inputFileList} ${configFile} "${extraOpts[@]}" commonOutputPath=${commonOutputPath} > benchmark.makeflow
-
+ cp benchmark.makeflow ${commonOutputPath}
makeflow ${makeflowOptions} benchmark.makeflow
- cd ../
else
echo "no makeflow!"
fi
+
+ #summarize the run based on the makeflow log
+ #and add it to the end of summary log
+ awk '/STARTED/ {startTime=$3}
+ /COMPLETED/ {endTime=$3}
+ END {print "makeflow running time: "(endTime-startTime)/1000000/3600" hours"}' \
+ benchmark.makeflow.makeflowlog | tee -a summary.log
+ paranoidCp summary.log ${commonOutputPath}
+
return 0
}
goGenerateMakeflow()
-{
+(
#generate the makeflow file
[[ $# -lt 3 ]] && echo "args: id inputFileList configFile" && return 1
productionID=${1}
configFile=${3}
shift 3
extraOpts=("$@")
+
+ #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
"runCalibTrain.C"
"runCPass0.sh"
"recCPass0.C"
+ "runQA.sh"
)
for file in ${inputFiles[*]}; do
[[ -f ${file} ]] && copyFiles+=("${file}")
declare -a arr_cpass0_outputs
declare -a arr_cpass1_outputs
+ #Header
+ echo "### Automatically generated on $(LANG=C date) ###"
+ echo ; echo
+
jobindex=0
inputFile=""
while read inputFile; do
if [[ ${autoOCDB} -ne 0 ]]; then
currentDefaultOCDB=$(setYear ${inputFile} ${defaultOCDB})
fi
+ guessRunData ${inputFile}
+
+ #Set variables
+ echo "### Variables ###"
+ echo "OUTPATH=\"${commonOutputPath}/${year}/${period}\""
+ echo ; echo
#CPass0
- arr_cpass0_outputs[${jobindex}]="${commonOutputPath}/meta/cpass0.job${jobindex}.run${runNumber}.done"
- echo "${arr_cpass0_outputs[${jobindex}]} : benchmark.sh ${configFile} ${copyFiles[@]}"
- echo -n " ${alirootEnv} ./benchmark.sh CPass0 ${commonOutputPath}/000${runNumber}/cpass0 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex}"" "
- for extraOption in "${extraOpts[@]}"; do echo -n \'${extraOption}\'" "; done; echo
- echo
+ #arr_cpass0_outputs[${jobindex}]="${commonOutputPath}/meta/cpass0.job${jobindex}.run${runNumber}.done"
+ arr_cpass0_outputs[${jobindex}]="cpass0.job${jobindex}.run${runNumber}.done"
+ echo "### CPass0 ###"
+ echo "${arr_cpass0_outputs[${jobindex}]}: benchmark.sh ${configFile} ${copyFiles[@]}"
+ echo " ${alirootEnv} ./benchmark.sh CPass0 \$OUTPATH/000${runNumber}/cpass0 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex} ${extraOpts[@]}"" "
+ echo ; echo
#CPass1
- arr_cpass1_outputs[${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 -n " ${alirootEnv} ./benchmark.sh CPass1 ${commonOutputPath}/000${runNumber}/cpass1 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex}"" "
- for extraOption in "${extraOpts[@]}"; do echo -n \'${extraOption}\'" "; done; echo
- echo
+ #arr_cpass1_outputs[${jobindex}]="${commonOutputPath}/meta/cpass1.job${jobindex}.run${runNumber}.done"
+ arr_cpass1_outputs[${jobindex}]="cpass1.job${jobindex}.run${runNumber}.done"
+ echo "### CPass1 ###"
+ echo "${arr_cpass1_outputs[${jobindex}]}: benchmark.sh ${configFile} cpass0.localOCDB.${runNumber}.tgz.done ${copyFiles[@]}"
+ echo " ${alirootEnv} ./benchmark.sh CPass1 \$OUTPATH/000${runNumber}/cpass1 ${inputFile} ${nEvents} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex} ${extraOpts[@]}"" "
+ echo ; echo
((jobindex++))
done< <(grep "/000${runNumber}/" ${inputFileList})
#CPass0 list of Calib files to merge
- arr_cpass0_calib_list[${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}]} ${arr_cpass0_outputs[*]}"
- echo
+ #arr_cpass0_calib_list[${runNumber}]="${commonOutputPath}/meta/cpass0.calib.run${runNumber}.list"
+ arr_cpass0_calib_list[${runNumber}]="cpass0.calib.run${runNumber}.list"
+ echo "### Produces the list of CPass0 files to merge (executes locally) ###"
+ echo "${arr_cpass0_calib_list[${runNumber}]}: benchmark.sh ${arr_cpass0_outputs[*]}"
+ echo " LOCAL ./benchmark.sh PrintValues calibfile ${arr_cpass0_calib_list[${runNumber}]} ${arr_cpass0_outputs[*]} && mkdir -p \$OUTPATH/meta && cp ${arr_cpass0_calib_list[${runNumber}]} \$OUTPATH/meta/${arr_cpass0_calib_list[${runNumber}]}"
+ echo ; echo
#CPass0 merging
- 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 -n " ${alirootEnv} ./benchmark.sh MergeCPass0 ${commonOutputPath}/000${runNumber}/cpass0 ${currentDefaultOCDB} ${configFile} ${runNumber} ${arr_cpass0_calib_list[${runNumber}]}"" "
- for extraOption in "${extraOpts[@]}"; do echo -n \'${extraOption}\'" "; done; echo
- echo
+ echo "### Merges CPass0 files ###"
+ #arr_cpass0_merged[${runNumber}]="${commonOutputPath}/meta/merge.cpass0.run${runNumber}.done"
+ arr_cpass0_merged[${runNumber}]="merge.cpass0.run${runNumber}.done"
+ echo "cpass0.localOCDB.${runNumber}.tgz.done ${arr_cpass0_merged[${runNumber}]}: benchmark.sh ${configFile} ${arr_cpass0_calib_list[${runNumber}]} ${copyFiles[@]}"
+ echo " ${alirootEnv} ./benchmark.sh MergeCPass0 \$OUTPATH/000${runNumber}/cpass0 ${currentDefaultOCDB} ${configFile} ${runNumber} ${arr_cpass0_calib_list[${runNumber}]} ${extraOpts[@]}"" "
+ echo ; echo
#CPass1 list of Calib/QA/ESD/filtered files
# the trick with QA is to have the string "Stage.txt" in the file name of the list of directories with QA output to trigger
# the production of the QA trending tree (only then the task->Finish() will be called in QAtrain_duo.C, on the grid
# this corresponds to the last merging stage)
- arr_cpass1_QA_list[${runNumber}]="${commonOutputPath}/meta/cpass1.QA.run${runNumber}.lastMergingStage.txt.list"
+ #arr_cpass1_QA_list[${runNumber}]="${commonOutputPath}/meta/cpass1.QA.run${runNumber}.lastMergingStage.txt.list"
+ arr_cpass1_QA_list[${runNumber}]="cpass1.QA.run${runNumber}.lastMergingStage.txt.list"
+ echo "### Lists CPass1 QA ###"
echo "${arr_cpass1_QA_list[${runNumber}]}: benchmark.sh ${arr_cpass1_outputs[*]}"
- echo " ./benchmark.sh PrintValues dir ${arr_cpass1_QA_list[${runNumber}]} ${arr_cpass1_outputs[*]}"
- echo
- arr_cpass1_calib_list[${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}]} ${arr_cpass1_outputs[*]};"
- echo
- arr_cpass1_ESD_list[${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}]} ${arr_cpass1_outputs[*]}"
- echo
- arr_cpass1_filtered_list[${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
+ echo " LOCAL ./benchmark.sh PrintValues dir ${arr_cpass1_QA_list[${runNumber}]} ${arr_cpass1_outputs[*]} && mkdir -p \$OUTPATH/meta && cp ${arr_cpass1_QA_list[${runNumber}]} \$OUTPATH/meta/${arr_cpass1_QA_list[${runNumber}]}"
+ echo ; echo
+
+ #arr_cpass1_calib_list[${runNumber}]="${commonOutputPath}/meta/cpass1.calib.run${runNumber}.list"
+ arr_cpass1_calib_list[${runNumber}]="cpass1.calib.run${runNumber}.list"
+ echo "### Lists CPass1 Calib ###"
+ echo "${arr_cpass1_calib_list[${runNumber}]}: benchmark.sh ${arr_cpass1_outputs[*]}"
+ echo " LOCAL ./benchmark.sh PrintValues calibfile ${arr_cpass1_calib_list[${runNumber}]} ${arr_cpass1_outputs[*]} && mkdir -p \$OUTPATH/meta && cp ${arr_cpass1_calib_list[${runNumber}]} \$OUTPATH/meta/${arr_cpass1_calib_list[${runNumber}]}"
+ echo ; echo
+
+ #arr_cpass1_ESD_list[${runNumber}]="${commonOutputPath}/meta/cpass1.ESD.run${runNumber}.list"
+ arr_cpass1_ESD_list[${runNumber}]="cpass1.ESD.run${runNumber}.list"
+ echo "### Lists CPass1 ESDs ###"
+ echo "${arr_cpass1_ESD_list[${runNumber}]}: benchmark.sh ${arr_cpass1_outputs[*]}"
+ echo " LOCAL ./benchmark.sh PrintValues esd ${arr_cpass1_ESD_list[${runNumber}]} ${arr_cpass1_outputs[*]} && mkdir -p \$OUTPATH/meta && cp ${arr_cpass1_ESD_list[${runNumber}]} \$OUTPATH/meta/${arr_cpass1_ESD_list[${runNumber}]}"
+ echo ; echo
+
+ #arr_cpass1_filtered_list[${runNumber}]="${commonOutputPath}/meta/cpass1.filtered.run${runNumber}.list"
+ arr_cpass1_filtered_list[${runNumber}]="cpass1.filtered.run${runNumber}.list"
+ echo "### Lists CPass1 filtered ###"
+ echo "${arr_cpass1_filtered_list[${runNumber}]}: benchmark.sh ${arr_cpass1_outputs[*]}"
+ echo " LOCAL ./benchmark.sh PrintValues filteredTree ${arr_cpass1_filtered_list[${runNumber}]} ${arr_cpass1_outputs[*]} && mkdir -p \$OUTPATH/meta && cp ${arr_cpass1_filtered_list[${runNumber}]} \$OUTPATH/meta/${arr_cpass1_filtered_list[${runNumber}]}"
+ echo ; 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 -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}]}"" "
- for extraOption in "${extraOpts[@]}"; do echo -n \'${extraOption}\'" "; done; echo
- echo
+ #arr_cpass1_merged[${runNumber}]="${commonOutputPath}/meta/merge.cpass1.run${runNumber}.done"
+ arr_cpass1_merged[${runNumber}]="merge.cpass1.run${runNumber}.done"
+ echo "### Merges CPass1 files ###"
+ echo "cpass1.localOCDB.${runNumber}.tgz.done ${arr_cpass1_merged[${runNumber}]}: benchmark.sh ${configFile} ${arr_cpass1_calib_list[${runNumber}]} ${arr_cpass1_QA_list[${runNumber}]} ${copyFiles[@]}"
+ echo " ${alirootEnv} ./benchmark.sh MergeCPass1 \$OUTPATH/000${runNumber}/cpass1 ${currentDefaultOCDB} ${configFile} ${runNumber} ${arr_cpass1_calib_list[${runNumber}]} ${arr_cpass1_QA_list[${runNumber}]} ${arr_cpass1_filtered_list[${runNumber}]} ${extraOpts[@]}"" "
+ echo ; echo
#CPass0 wrapped in a profiling tool (valgrind,....)
if [[ -n ${profilingCommand} ]]; then
- arr_cpass0_profiled_outputs[${runNumber}]="${commonOutputPath}/meta/cpass0.jobProfiled.run${runNumber}.done"
- echo "${arr_cpass0_profiled_outputs[${runNumber}]} : benchmark.sh ${configFile} ${copyFiles[@]}"
- echo -n " ${alirootEnv} ./benchmark.sh CPass0 ${commonOutputPath}/000${runNumber}/profiled ${inputFile} ${nEventsProfiling} ${currentDefaultOCDB} ${configFile} ${runNumber} profiling"" "
- for extraOption in "${extraOpts[@]}"; do echo -n \'${extraOption}\'" "; done;
- echo "\"useProfilingCommand=${profilingCommand}\""
- echo
+ inputFile=$(grep -m1 "${runNumber}/" ${inputFileList})
+ [[ -z ${nEventsProfiling} ]] && nEventsProfiling=2
+ currentDefaultOCDB=$(setYear ${inputFile} ${defaultOCDB})
+ jobindex="profiling"
+
+ #arr_cpass0_profiled_outputs[${runNumber}]="${commonOutputPath}/meta/profiling.cpass0.job${jobindex}.run${runNumber}.done"
+ arr_cpass0_profiled_outputs[${runNumber}]="profiling.cpass0.job${jobindex}.run${runNumber}.done"
+ echo "### CPass0 in a profiler ###"
+ echo "${arr_cpass0_profiled_outputs[${runNumber}]}: benchmark.sh ${configFile} ${copyFiles[@]}"
+ profilingCommand=$(encSpaces "${profilingCommand}")
+ echo " ${alirootEnv} ./benchmark.sh CPass0 \$OUTPATH/000${runNumber}/${jobindex} ${inputFile} ${nEventsProfiling} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex} ${extraOpts[@]} useProfilingCommand=${profilingCommand}"
+ echo ; echo
fi
done #runs
#Summary
- echo "${commonOutputPath}/summary.log : benchmark.sh ${configFile} ${arr_cpass1_merged[*]}"
- echo -n " ${alirootEnv} ./benchmark.sh MakeSummary ${configFile}"" "
- for extraOption in "${extraOpts[@]}"; do echo -n \'${extraOption}\'" "; done; echo
- echo
+ echo "### Summary ###"
+ echo "summary.log: benchmark.sh ${configFile} ${arr_cpass1_merged[*]}"
+ echo " ${alirootEnv} ./benchmark.sh MakeSummary ${configFile} ${extraOpts[@]}"
+ echo ; echo
return 0
-}
+)
goPrintValues()
-{
+(
#print the values given the key from any number of files (store in output file on second argument)
if [[ $# -lt 3 ]]; then
echo "goPrintValues key outputFile inputFiles"
- echo "if outputFile is \"-\" dont redirect to a file"
+ echo "if outputFile is \"-\" don't redirect to a file"
return
fi
key=${1}
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
- if ! parseConfig ${configFile} ${@}; then return 1; fi
+ 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}
cd ${outputDir}
[[ ! "${PWD}" =~ "${outputDir}" ]] && echo "PWD is not equal to outputDir=${outputDir}" && cd ${olddir} && return 1
- ${ALICE_ROOT}/PWGPP/QA/scripts/runQA.sh inputList="${mergedQAfileList}" inputListHighPtTrees="${filteringList}"
+ inputFiles=(
+ "${batchWorkingDirectory}/runQA.sh"
+ "${ALICE_ROOT}/PWGPP/QA/scripts/runQA.sh"
+ )
+ for file in ${inputFiles[*]}; do
+ [[ ! -f ${file##*/} && -f ${file} ]] && echo "copying ${file}" && cp -f ${file} .
+ done
+ echo "running QA with command:"
+ echo ./runQA.sh inputList="${mergedQAfileList}" inputListHighPtTrees="${filteringList}" ocdbStorage="${defaultOCDB}"
+ ./runQA.sh inputList="${mergedQAfileList}" inputListHighPtTrees="${filteringList}" ocdbStorage="${defaultOCDB}"
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
done
echo ${runNumber}
return 0
-}
+)
validateLog()
-{
+(
log=${1}
errorConditions=(
'There was a crash'
fi
return 0
-}
+)
summarizeLogs()
-{
+(
#print a summary of logs
logFiles=(
"*.log"
"stderr"
)
+ #put dir information in the output
+ echo "dir $PWD"
+
#check logs
local logstatus=0
for log in ${logFiles[*]}; do
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=${2}
#get path to input list
#record the working directory provided by the batch system
batchWorkingDirectory=${PWD}
+ [[ -z ${commonOutputPath} ]] && commonOutputPath=${PWD}
+ doneFileBase=filtering.cpass1.run${runNumber}.done
+ doneFileTmp=${batchWorkingDirectory}/${doneFileBase}
+ doneFile=${commonOutputPath}/meta/${doneFileBase}
- commonOutputPath=${PWD}
- doneFile=${commonOutputPath}/meta/filtering.cpass1.run${runNumber}.done
-
- runpath=${outputDir}
- [[ ${reconstructInTemporaryDir} -eq 1 && -n ${TMPDIR} ]] && runpath=${TMPDIR}
- [[ ${reconstructInTemporaryDir} -eq 1 && -z ${TMPDIR} ]] && runpath=$(mktemp -d)
-
-
- [[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
-
- mkdir -p ${outputDir}
- mkdir -p ${runpath}
-
- cd ${runpath}
- [[ ! ${PWD} =~ ${runpath} ]] && echo "PWD=$PWD is not the runpath=${runpath}" && touch ${doneFile} && return 1
-
cat > filtering.log << EOF
goMakeFilteredTrees config:
runpath=${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 ${runpath}
+
+ cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
+ [[ -n ${removeTMPdoneFile} ]] && rm -f ${doneFileTmp}
+
return 0
-}
+)
submit()
{
waitForJOBID=${4}
command=${5}
shift 5
- commandArgs=("$@")
+ local commandArgs=("$@")
#add quote strings around the extra arguments
for ((i=0; i<${#commandArgs[@]}; i++)); do
productionID=${1}
inputList=${2}
configFile=${3:-"benchmark.config"}
- configFile=$(readlink -f ${configFile})
+ #if which greadlink; then configFile=$(greadlink -f ${configFile}); fi
shift 3
extraOpts=("$@")
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 "${extraOpts[i]}")
+ done
+ extraOpts+=("encodedSpaces=1")
+ #this removes the copy of the done file used by makeflow (in the running dir)
+ extraOpts+=("removeTMPdoneFile=1")
+
#record the working directory provided by the batch system
batchWorkingDirectory=${PWD}
[[ ! -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 ###"
JOBfilterESDcpass1="fp1_${JOBpostfix}"
LASTJOB="000"
- oneInputFile=$(egrep -m1 "${runNumber}\/" ${inputList})
+ oneInputFile=$(egrep -m1 "${runNumber}/" ${inputList})
currentDefaultOCDB=${defaultOCDB}
[[ -z ${autoOCDB} ]] && autoOCDB=1
if [[ ${autoOCDB} -ne 0 ]]; then
currentDefaultOCDB=$(setYear ${oneInputFile} ${defaultOCDB})
fi
+ period=$(guessPeriod ${oneInputFile})
+ year=$(guessYear ${oneInputFile})
echo "submitting run ${runNumber} with OCDB ${currentDefaultOCDB}"
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} "${extraOpts[@]}"
+ submit "profile-${JOBpostfix}" 1 1 000 "${alirootEnv} ${self}" CPass0 ${commonOutputPath}/${year}/${period}/000${runNumber}/${jobindex} ${oneInputFile} ${nEventsProfiling} ${currentDefaultOCDB} ${configFile} ${runNumber} ${jobindex} useProfilingCommand=$(encSpaces "${profilingCommand}") "${extraOpts[@]}"
fi
################################################################################
echo
# create directory and copy all files that are needed
- targetDirectory="${commonOutputPath}/000${runNumber}/cpass0"
+ targetDirectory="${commonOutputPath}/${year}/${period}/000${runNumber}/cpass0"
mkdir -p ${targetDirectory}
filesCPass0=(
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} ${maxSecondsToWait}
LASTJOB=${JOBID1wait}
fi #end running CPass0
echo "submit CPass0 merging for run ${runNumber}"
echo
- targetDirectory="${commonOutputPath}/000${runNumber}/cpass0"
+ targetDirectory="${commonOutputPath}/${year}/${period}/000${runNumber}/cpass0"
mkdir -p ${targetDirectory}
#copy the scripts
if [ ${runCPass1reco} -eq 1 ]; then
- targetDirectory="${commonOutputPath}/000${runNumber}/cpass1"
+ targetDirectory="${commonOutputPath}/${year}/${period}/000${runNumber}/cpass1"
rm -f ${commonOutputPath}/meta/cpass1.job*.run${runNumber}.done
# safety feature: if we are re-running for any reason we want to delete the previous output first.
################################################################################
## 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} ${maxSecondsToWait}
LASTJOB=${JOBID4wait}
################################################################################
echo "submit CPass1 merging for run ${runNumber}"
echo
- targetDirectory="${commonOutputPath}/000${runNumber}/cpass1"
+ targetDirectory="${commonOutputPath}/${year}/${period}/000${runNumber}/cpass1"
rm -f ${commonOutputPath}/meta/merge.cpass1.run${runNumber}.done
mkdir -p ${targetDirectory}
# 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[@]}"
+ # submit "${JOBfilterESDcpass1}" 1 1 "${JOBmakeESDlistCPass1}" "${alirootEnv} ${self}" MakeFilteredTrees ${commonOutputPath}/${year}/${period}/000${runNumber}/cpass1 ${runNumber} ${commonOutputPath}/meta/cpass1.ESD.run${runNumber}.list ${filteringFactorHighPt} ${filteringFactorV0s} ${currentDefaultOCDB} 1000000 0 10000000 0 ${configFile} AliESDs_Barrel.root "${extraOpts[@]}"
# LASTJOB=${JOBfilterESDcpass1}
#fi
echo "submit make a summary"
echo
- submit "${JOBID6}" 1 1 "${LASTJOB}" "${alirootEnv} ${self}" MakeSummary ${configFile}
+ [[ -z ${alirootEnvQA} ]] && alirootEnvQA=$(encSpaces "${alirootEnv}")
+ submit "${JOBID6}" 1 1 "${LASTJOB}" "${alirootEnvQA} ${self}" MakeSummary ${configFile} "commonOutputPath=${commonOutputPath}"
LASTJOB=${JOBID6}
#################################################################################
}
goWaitForOutput()
-{
+(
umask 0002
[[ $# -lt 3 ]] && echo "goWaitForOutput() wrong number of arguments, exiting.." && return 1
echo searchPath=${1}
fileName=${2}
numberOfFiles=${3}
maxSecondsToWait=${4}
- extraFindOptions=${5}
- echo "command to be executed: /bin/ls -1 ${searchPath}/${fileName} ${extraFindOptions}"
+ echo "command to be executed: /bin/ls -1 ${searchPath}/${fileName}"
[[ -z "${maxSecondsToWait}" ]] && maxSecondsToWait=$(( 3600*12 ))
while true; do
- #n=$(find ${searchPath} ${extraFindOptions} -name "${fileName}" | wc -l)
n=$(/bin/ls -1 ${searchPath}/${fileName} 2>/dev/null | wc -l)
[[ ${n} -gt 0 ]] && echo "found ${n} X ${fileName}"
[[ ${n} -ge ${numberOfFiles} ]] && break
done
echo "DONE! exiting..."
return 0
-}
+)
mergeSysLogs()
-{
+(
outputFile=${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
aliroot -b -q "mergeTree.C" > mergeTrees.log
return $?
-}
+)
+
+stackTraceTree()
+(
+ if [[ $# -lt 1 ]]; then
+ echo 'make stacktrace processing in case of standard root crash log'
+ echo 'input is a (list of) text files with the stack trace (either gdb aoutput'
+ echo 'produced with e.g. gdb --batch --quiet -ex "bt" -ex "quit" aliroot core,'
+ echo 'or the root crash log), output is a TTree formatted table.'
+ echo 'example usage:'
+ echo 'benchmark.sh stackTraceTree /foo/*/rec.log'
+ echo 'benchmark.sh stackTraceTree $(cat file.list)'
+ echo 'benchmark.sh stackTraceTree `cat file.list`'
+ return 0
+ fi
+ gawk '
+ BEGIN {
+ print "frame/I:method/C:line/C:cpass/I:aliroot/I:file/C";
+ RS="#[0-9]*";
+ aliroot=0;
+ read=1;
+ }
+ /There was a crash/ {read=1;}
+ /The lines below might hint at the cause of the crash/ {read=0;}
+ read==1 {
+ if ($3 ~ /Ali*/) aliroot=1; else aliroot=0;
+ gsub("#","",RT);
+ if ($NF!="" && RT!="" && $3!="") print RT" "$3" "$NF" "0" "aliroot" "FILENAME
+ }
+ ' "$@" 2>/dev/null
+)
goMakeSummary()
-{
+(
#all the final stuff goes in here for ease of use:
# summary logs
# qa plot making
# final file lists
+ # runs in current dir - in makeflow mode it can run LOCAL, then the QA plots and summaries
+ # will appear in the submission dir.
#some defaults:
log="summary.log"
productionID="qa"
extraOpts=("$@")
if ! parseConfig ${configFile} "${extraOpts[@]}"; then return 1; fi
- configFile=$(readlink -f ${configFile})
+ #if which greadlink; then configFile=$(greadlink -f ${configFile}); fi
#record the working directory provided by the batch system
batchWorkingDirectory=${PWD}
+
+ logTmp=${batchWorkingDirectory}/${log}
+ logDest=${commonOutputPath}/${log}
[[ -f ${alirootSource} && -z ${ALICE_ROOT} ]] && source ${alirootSource}
#copy some useful stuff
#and go to the commonOutputPath
cp ${configFile} ${commonOutputPath}
- cd ${commonOutputPath}
- exec &> >(tee ${log})
+ exec &> >(tee ${logTmp})
#summarize the global stuff
echo "env script: ${alirootSource} ${alirootEnv}"
echo "commonOutputPath=${commonOutputPath}"
#summarize the stacktraces
- awk '
- BEGIN {
- print "frame/I:method/C:line/C:cpass/I:aliroot/I";
- RS="#[0-9]*";
- aliroot=0;
- }
- {
- if ($3 ~ /Ali*/) aliroot=1; else aliroot=0;
- gsub("#","",RT);
- if ($NF!="" && RT!="" && $3!="") print RT" "$3" "$NF" "0" "aliroot
- }
- ' 000*/cpass0/*/stacktrace* 2>/dev/null > stacktrace.tree
- awk '
- BEGIN {
- RS="#[0-9]*";
- aliroot=0;
- }
- {
- if ($3 ~ /Ali*/) aliroot=1; else aliroot=0;
- gsub("#","",RT);
- if ($NF!="" && RT!="" && $3!="") print RT" "$3" "$NF" "1" "aliroot
- }
- ' 000*/cpass1/*/stacktrace* 2>/dev/null >> stacktrace.tree
+ stackTraceTree ${commonOutputPath}/*/*/000*/cpass0/*/stacktrace* > stacktrace_cpass0.tree
+ stackTraceTree ${commonOutputPath}/*/*/000*/cpass1/*/stacktrace* > stacktrace_cpass1.tree
echo total numbers for the production:
echo
awk 'BEGIN {nFiles=0;nCore=0;}
/^calibfile/ {nFiles++;}
/core dumped/ {nCore++i;}
- END {print "cpass0 produced "nFiles" calib files, "nCore" core files";}' meta/cpass0.job*done 2>/dev/null
+ END {print "cpass0 produced "nFiles" calib files, "nCore" core files";}' ${commonOutputPath}/meta/cpass0.job*done 2>/dev/null
awk 'BEGIN {nOK=0; nBAD=0; }
/\/rec.log OK/ {nOK++;}
/\/rec.log BAD/ {nBAD++;}
/stderr BAD/ {if ($0 ~ /rec.log/){nBAD++;}}
- END {print "cpass0 reco: OK: "nOK"\tBAD: "nBAD;}' meta/cpass0.job*done 2>/dev/null
+ END {print "cpass0 reco: OK: "nOK"\tBAD: "nBAD;}' ${commonOutputPath}/meta/cpass0.job*done 2>/dev/null
awk 'BEGIN {nOK=0; nBAD=0; }
/\/calib.log OK/ {nOK++;}
/\/calib.log BAD/ {nBAD++;}
- END {print "cpass0 calib: OK: "nOK"\tBAD: "nBAD;}' meta/cpass0.job*done 2>/dev/null
+ END {print "cpass0 calib: OK: "nOK"\tBAD: "nBAD;}' ${commonOutputPath}/meta/cpass0.job*done 2>/dev/null
awk 'BEGIN {nOK=0; nBAD=0; }
/merge.log OK/ {nOK++;}
/merge.log BAD/ {nBAD++;}
- END {print "cpass0 merge: OK: "nOK"\tBAD: "nBAD;}' meta/merge.cpass0*done 2>/dev/null
+ END {print "cpass0 merge: OK: "nOK"\tBAD: "nBAD;}' ${commonOutputPath}/meta/merge.cpass0*done 2>/dev/null
awk 'BEGIN {nOK=0; nBAD=0; }
/ocdb.log OK/ {nOK++;}
/ocdb.log BAD/ {nBAD++;}
- END {print "cpass0 OCDB: OK: "nOK"\tBAD: "nBAD;}' meta/merge.cpass0*done 2>/dev/null
+ END {print "cpass0 OCDB: OK: "nOK"\tBAD: "nBAD;}' ${commonOutputPath}/meta/merge.cpass0*done 2>/dev/null
echo
awk 'BEGIN {nFiles=0;nCore=0;}
/^calibfile/ {nFiles++;}
/core dumped/ {nCore++;}
- END {print "cpass1 produced "nFiles" calib files, "nCore" core files";}' meta/cpass1.job*done 2>/dev/null
+ END {print "cpass1 produced "nFiles" calib files, "nCore" core files";}' ${commonOutputPath}/meta/cpass1.job*done 2>/dev/null
awk 'BEGIN {nOK=0; nBAD=0; }
/\/rec.log OK/ {nOK++;}
/\/rec.log BAD/ {nBAD++;}
/stderr BAD/ {if ($0 ~ /rec.log/){nBAD++;}}
- END {print "cpass1 reco: OK: "nOK"\tBAD: "nBAD;}' meta/cpass1.job*done 2>/dev/null
+ END {print "cpass1 reco: OK: "nOK"\tBAD: "nBAD;}' ${commonOutputPath}/meta/cpass1.job*done 2>/dev/null
awk 'BEGIN {nOK=0; nBAD=0; }
/\/calib.log OK/ {nOK++;}
/\/calib.log BAD/ {nBAD++;}
- END {print "cpass1 calib: OK: "nOK"\tBAD: "nBAD;}' meta/cpass1.job*done 2>/dev/null
+ END {print "cpass1 calib: OK: "nOK"\tBAD: "nBAD;}' ${commonOutputPath}/meta/cpass1.job*done 2>/dev/null
awk 'BEGIN {nOK=0; nBAD=0; }
/merge.log OK/ {nOK++;}
/merge.log BAD/ {nBAD++;}
- END {print "cpass1 merge: OK: "nOK"\tBAD: "nBAD;}' meta/merge.cpass1*done 2>/dev/null
+ END {print "cpass1 merge: OK: "nOK"\tBAD: "nBAD;}' ${commonOutputPath}/meta/merge.cpass1*done 2>/dev/null
awk 'BEGIN {nOK=0; nBAD=0; }
/ocdb.log OK/ {nOK++;}
/ocdb.log BAD/ {nBAD++;}
- END {print "cpass1 OCDB: OK: "nOK"\tBAD: "nBAD;}' meta/merge.cpass1*done 2>/dev/null
+ END {print "cpass1 OCDB: OK: "nOK"\tBAD: "nBAD;}' ${commonOutputPath}/meta/merge.cpass1*done 2>/dev/null
echo
echo per run stats:
- /bin/ls -1 meta/merge.cpass0.run*.done | while read x
+ /bin/ls -1 ${commonOutputPath}/meta/merge.cpass0.run*.done | while read x
do
- dir=$(goPrintValues calibfile - ${x})
+ dir=$(goPrintValues dir - ${x})
runNumber=$(guessRunNumber ${dir})
[[ -z ${runNumber} ]] && continue
- if $(/bin/ls meta/cpass0.job*.run${runNumber}.done &> /dev/null); then
+ if $(/bin/ls ${commonOutputPath}/meta/cpass0.job*.run${runNumber}.done &> /dev/null); then
statusCPass0=( $(
awk 'BEGIN {nOKrec=0;nBADrec=0;nOKcalib=0;nBADcalib=0;nOKstderr=0;nBADstderr=0;}
/\/rec.log OK/ {nOKrec++;}
/stderr OK/ {nOKstderr++;}
/\/calib.log OK/ {nOKcalib++;}
/\/calib.log BAD/ {nBADcalib++}
- END {print ""nOKrec" "nBADrec" "nOKstderr" "nBADstderr" "nOKcalib" "nBADcalib;}' meta/cpass0.job*.run${runNumber}.done 2>/dev/null
+ END {print ""nOKrec" "nBADrec" "nOKstderr" "nBADstderr" "nOKcalib" "nBADcalib;}' ${commonOutputPath}/meta/cpass0.job*.run${runNumber}.done 2>/dev/null
) )
fi
- if $(/bin/ls meta/cpass1.job*.run${runNumber}.done &>/dev/null); then
+ if $(/bin/ls ${commonOutputPath}/meta/cpass1.job*.run${runNumber}.done &>/dev/null); then
statusCPass1=( $(
awk 'BEGIN {nOKrec=0;nBADrec=0;nOKcalib=0;nBADcalib=0;nOKstderr=0;nBADstderr=0;nQAbarrelOK=0;nQAbarrelBAD=0;nQAouterOK=0;nQAouterBAD=0;}
/\/rec.log OK/ {nOKrec++;}
/\/qa_barrel.log BAD/ {nQAbarrelBAD++;}
/\/qa_outer.log OK/ {nQAouterOK++;}
/\/qa_outer.log BAD/ {nQAouterBAD++;}
- END {print ""nOKrec" "nBADrec" "nOKstderr" "nBADstderr" "nOKcalib" "nBADcalib" "nQAbarrelOK" "nQAbarrelBAD" "nQAouterOK" "nQAouterBAD;}' meta/cpass1.job*.run${runNumber}.done 2>/dev/null
+ END {print ""nOKrec" "nBADrec" "nOKstderr" "nBADstderr" "nOKcalib" "nBADcalib" "nQAbarrelOK" "nQAbarrelBAD" "nQAouterOK" "nQAouterBAD;}' ${commonOutputPath}/meta/cpass1.job*.run${runNumber}.done 2>/dev/null
) )
fi
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
+ rm -f trending.root
+ goMerge trending.list trending.root ${configFile} "${extraOpts[@]}" &> mergeTrending.log
goMakeSummaryTree ${commonOutputPath} 0
goMakeSummaryTree ${commonOutputPath} 1
goMakeMergedSummaryTree
#if set, email the summary
- [[ -n ${MAILTO} ]] && cat ${log} | mail -s "benchmark ${productionID} done" ${MAILTO}
+ [[ -n ${MAILTO} ]] && cat ${logTmp} | mail -s "benchmark ${productionID} done" ${MAILTO}
+
+ # Copy log to destination (delete all on failure to signal error)
+ cp "$logTmp" "$logDest" || rm -f "$logTmp" "$logDest"
+
+ #copy output files
+ exec &> >(tee fileCopy.log)
+ paranoidCp QAplots ${commonOutputPath}
+ paranoidCp *.list ${commonOutputPath}
+ paranoidCp *.root ${commonOutputPath}
+ paranoidCp *.log ${commonOutputPath}
+ paranoidCp fileCopy.log ${commonOutputPath}
return 0
-}
+)
goMakeSummaryTree()
-{
+(
if [[ $# -lt 1 ]] ; then
return
fi
done
return 0
-}
+)
parseConfig()
{
shift
args=("$@")
+
#some defaults
#autoOCDB=0
defaultOCDB="raw://"
#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 "
+ batchFlags=""
baseOutputDirectory="$PWD/output"
#alirootEnv="/cvmfs/alice.cern.ch/bin/alienv setenv AliRoot/v5-04-34-AN -c"
#alirootEnv="/home/mkrzewic/alisoft/balice_master.sh"
#dontRedirectStdOutToLog=1
logToFinalDestination=1
ALIROOT_FORCE_COREDUMP=1
+ pretendDelay=0
+ copyInputData=0
#first, source the config file
if [ -f ${configFile} ]; then
source ${configFile}
else
- echo "config file ${configFile} not found!, skipping..."
+ echo "config file ${configFile} not found!"
+ return 1
fi
unset encodedSpaces
for opt in "${args[@]}"; do
- [[ "${opt}" =~ encodedSpaces=.* ]] && encodedSpaces=1 && break
+ [[ "${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 ${var}, should be: option=value, stopping..."
+ echo "badly formatted option \"${opt}\" should be: option=value, stopping..."
return 1
fi
local var="${opt%%=*}"
local value="${opt#*=}"
- [[ -n ${encodedSpaces} ]] && value=$(decSpaces "${value}")
- echo "${var} = ${value}"
+ echo "${var}=${value}"
export ${var}="${value}"
done
[[ -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
+ [[ $(type -t aliroot) =~ "function" ]] && export -f aliroot && echo "exporting aliroot() function..."
return 0
}
aliroot()
{
- args="$@"
+ args=("$@")
if [[ -n ${useProfilingCommand} ]]; then
- valgrindLogFile="cpu.txt"
- [[ "${args}" =~ rec ]] && valgrindLogFile="cpu_rec.txt"
- [[ "${args}}" =~ Calib ]] && valgrindLogFile="cpu_calib.txt"
- [[ -n ${useProfilingCommand} ]] && useProfilingCommand="${useProfilingCommand} --log-file=${valgrindLogFile}"
- echo running ${useProfilingCommand} aliroot ${args}
- ${useProfilingCommand} aliroot ${args}
+ profilerLogFile="cpu.txt"
+ [[ "${args[@]}" =~ rec ]] && profilerLogFile="cpu_rec.txt"
+ [[ "${args[@]}" =~ Calib ]] && profilerLogFile="cpu_calib.txt"
+ echo running "${useProfilingCommand} aliroot ${args[@]} &> ${profilerLogFile}"
+ ${useProfilingCommand} aliroot "${args[@]}" &> ${profilerLogFile}
else
#to prevent an infinite recursion use "command aliroot" to disable
#aliases and functions
- echo running command aliroot ${args}
- command aliroot "$@"
+ echo running command aliroot "${args[@]}"
+ command aliroot "${args[@]}"
fi
return 0
}
+copyFileToLocal()
+(
+ #copies a file from either a remote or local location to a local destination
+ src="$1"
+ dst="$2"
+
+ proto="${src%%://*}"
+ if [[ "$proto" == "$src" ]]; then
+ cp "$src" "$dst"
+ else
+ case "$proto" in
+ root)
+ xrdcp -f "$src" "$dst"
+ ;;
+ http)
+ curl -L "$src" -O "$dst"
+ ;;
+ *)
+ echo "protocol not supported: $proto"
+ return 1
+ ;;
+ esac
+ fi
+)
+
+paranoidCp()
+(
+ #recursively copy files and directories
+ #to avoid using find and the like as they kill
+ #the performance on some cluster file systems
+ #does not copy links to avoid problems
+ sourceFiles=("${@}")
+ destination="${sourceFiles[@]:(-1)}" #last element
+ unset sourceFiles[${#sourceFiles[@]}-1] #remove last element (dst)
+ for src in "${sourceFiles[@]}"; do
+ if [[ -f "${src}" && ! -h "${src}" ]]; then
+ paranoidCopyFile "${src}" "${destination}"
+ elif [[ -d "${src}" && ! -h "${src}" ]]; then
+ src="${src%/}"
+ dst="${destination}/${src##*/}"
+ mkdir -p "${dst}"
+ paranoidCp "${src}"/* "${dst}"
+ fi
+ done
+)
+
+paranoidCopyFile()
+(
+ #copy a single file to a target in an existing dir
+ #repeat a few times if copy fails
+ src="${1}"
+ dst="${2}"
+ [[ -d "${dst}" ]] && dst="${dst}/${src##*/}"
+ [[ -z "${maxCopyTries}" ]] && maxCopyTries=5
+ #echo "maxCopyTries=${maxCopyTries}"
+ echo "cp ${src} ${dst}"
+ cp "${src}" "${dst}"
+ i=0
+ until cmp -s "${src}" "${dst}"; do
+ echo "try: ${i}"
+ [[ -f "${dst}" ]] && rm "${dst}"
+ cp "${src}" "${dst}"
+ [[ ${i} -gt ${maxCopyTries} ]] && ret=1 && return 1
+ (( i++ ))
+ done
+ return 0
+)
+
guessRunData()
{
#guess the period from the path, pick the rightmost one
#these functions encode strings to and from a space-less form
#use when spaces are not well handled (e.g. in arguments to
#commands in makeflow files, etc.
-encSpaces()(a="${1//,/\\,}";echo "${a// /,}")
-decSpaces()(a="${1//\\,/\\ }";b="${a//,/ }";echo "${b//\\ /,}")
+encSpaces()(echo "${1// /@@@@}")
+decSpaces()(echo "${1//@@@@/ }")
main "$@"
git://git.uio.no / u / mrichter / AliRoot.git / blobdiff