PWGPP/QA/scripts/runQA.sh

   1 #!/bin/bash
   2 main()
   3 {
   4   if [[ -z $1 ]]; then
   5     echo "Usage: "
   6     echo "  ${0##*/} option=value [option=value]"
   7     echo "  at least inputList should be specified, or configFile containing it:"
   8     echo "  ${0##*/} inputList=file.list"
   9     echo "  options override config file (if any), e.g.:"
  10     echo "  ${0##*/} configFile=runQA.config inputList=file.list outputDirectory=%det"
  11     return 1
  12   fi
  13
  14   if ! parseConfig $@; then
  15     ${0}
  16     return 1
  17   fi
  18
  19   [[ -z $ALICE_ROOT ]] && echo "ALICE_ROOT not defined" && return 1
  20
  21   ocdbregex='raw://'
  22   if [[ ${ocdbStorage} =~ ${ocdbregex} ]]; then
  23     alien-token-init
  24   fi
  25
  26   updateQA $@
  27 }
  28
  29 updateQA()
  30 {
  31   umask 0002
  32   parseConfig $@
  33
  34   #be paranoid and make some full paths
  35   [[ ! -f ${inputList} ]] && echo "no input list: ${inputList}" && return 1
  36   inputList=$(get_realpath ${inputList})
  37   mkdir -p ${workingDirectory}
  38   workingDirectory=$(workingDirectory=${workingDirectory%/}; cd ${workingDirectory%/*}; echo "${PWD}/${workingDirectory##*/}")
  39   if [[ ! -d ${workingDirectory} ]]; then
  40     echo "working dir $workingDirectory does not exist and cannot be created"
  41     return 1
  42   fi
  43   cd ${workingDirectory}
  44
  45   echo JOB config:
  46   echo inputList=$inputList
  47   echo outputDirectory=$outputDirectory
  48   echo
  49
  50   dateString=$(date +%Y-%m-%d-%H-%M)
  51   echo "Start time QA process: $dateString"
  52
  53   #logging
  54   mkdir -p $logDirectory
  55   [[ ! -d $logDirectory ]] && echo "no log dir $logDirectory" && return 1
  56   logFile="$logDirectory/${0##*/}.${dateString}.log"
  57   touch ${logFile}
  58   [[ ! -f ${logFile} ]] && echo "cannot write logfile $logfile" && return 1
  59   echo "logFile = $logFile"
  60   exec &>${logFile}
  61
  62   #check lock
  63   lockFile=${logDirectory}/runQA.lock
  64   [[ -f ${lockFile} ]] && echo "lock ${lockFile} exists!" && return 1
  65   touch ${lockFile}
  66   [[ ! -f ${lockFile} ]] && echo "cannot lock $lockFile" && return 1
  67
  68   ################################################################
  69   #ze detector loop
  70   for detectorScript in $ALICE_ROOT/PWGPP/QA/detectorQAscripts/*; do
  71
  72     [[ ! ${detectorScript} =~ .*\.sh ]] && continue
  73     detector=${detectorScript%.sh}
  74     detector=${detector##*/}
  75
  76     #skip if excluded
  77     if [[ "${excludeDetectors}" =~ ${detector} ]]; then
  78       echo "${detector} is excluded in config, skipping..."
  79       continue
  80     fi
  81
  82     #if includeDetectors set, only process thoe detectors specified there
  83     if [[ -n ${includeDetectors} && ! "${includeDetectors}" =~ ${detector} ]]; then
  84       echo "${detector} not included in includeDetectors, skipping..."
  85       continue
  86     fi
  87
  88     logSummary=${logDirectory}/summary-${detector}-${dateString}.log
  89     outputDir=$(substituteDetectorName ${detector} ${outputDirectory})
  90     tmpDetectorRunDir=${workingDirectory}/tmpQAtmpRunDir${detector}
  91     if ! mkdir -p ${tmpDetectorRunDir}; then
  92       echo "cannot create the temp dir $tmpDetectorRunDir"
  93       continue
  94     fi
  95     cd ${tmpDetectorRunDir}
  96
  97     tmpPrefix=${tmpDetectorRunDir}/${outputDir}
  98     echo
  99     echo "##############################################"
 100     echo "running QA for ${detector}"
 101     echo "  outputDir=$outputDir"
 102     echo "  tmpPrefix=$tmpPrefix"
 103
 104     unset -f runLevelQA
 105     unset -f periodLevelQA
 106     source ${detectorScript}
 107
 108     #################################################################
 109     #produce the QA and trending tree for each file (run)
 110     unset arrOfTouchedProductions
 111     declare -A arrOfTouchedProductions
 112     while read qaFile; do
 113       echo
 114
 115       if ! guessRunData ${qaFile}; then
 116         echo "could not guess run data from ${qaFile}"
 117         continue
 118       fi
 119
 120       tmpProductionDir=${tmpPrefix}/${dataType}/${year}/${period}/${pass}
 121       arrOfTouchedProductions[${tmpProductionDir}]=1
 122       tmpRunDir=${tmpProductionDir}/000${runNumber}
 123       mkdir -p ${tmpRunDir}
 124       cd ${tmpRunDir}
 125
 126       #handle the case of a zip archive
 127       [[ "$qaFile" =~ .*.zip$ ]] && qaFile="${qaFile}#QAresults.root"
 128       [[ "$qaFile" =~ .*.zip$ ]] && highPtTree="${qaFile}#FilterEvents_Trees.root"
 129
 130       echo running ${detector} runLevelQA for run ${runNumber} from ${qaFile}
 131       runLevelQA ${qaFile} &> runLevelQA.log
 132
 133       #perform some default actions:
 134       #if trending.root not created, create a default one
 135       if [[ ! -f trending.root ]]; then
 136         aliroot -b -q -l "$ALICE_ROOT/PWGPP/macros/simpleTrending.C(\"${qaFile}\",${runNumber},\"${detector}\",\"trending.root\",\"trending\",\"recreate\")" &>> runLevelQA.log
 137       fi
 138       cd ${tmpDetectorRunDir}
 139
 140     done < ${inputList}
 141
 142     #################################################################
 143     #cache which productions were (re)done
 144     echo "list of processed productions:"
 145     echo "    ${!arrOfTouchedProductions[@]}"
 146     echo
 147
 148     #################################################################
 149     #(re)do the merging/trending in the final destination
 150     for tmpProductionDir in ${!arrOfTouchedProductions[@]}; do
 151       echo
 152       echo "running period level stuff in ${tmpProductionDir}"
 153
 154       productionDir=${outputDir}/${tmpProductionDir#${tmpPrefix}}
 155
 156       mkdir -p ${productionDir}
 157       if [[ ! -d ${productionDir} ]]; then
 158         echo "cannot make productionDir $productionDir" && continue
 159       fi
 160       cd ${productionDir}
 161
 162       #move to final destination
 163       for dir in ${tmpProductionDir}/*; do
 164         oldRunDir=${outputDir}/${dir#${tmpPrefix}}
 165         if ! guessRunData "${dir}/dummyName"; then
 166           echo "could not guess run data from ${dir}"
 167           continue
 168         fi
 169
 170         #before moving - VALIDATE!!!
 171         if ! validate ${dir}; then continue; fi
 172
 173         if [[ -d ${oldRunDir} ]]; then
 174           echo "removing old ${oldRunDir}"
 175           rm -rf ${oldRunDir}
 176         fi
 177         echo "moving new ${runNumber} to ${productionDir}"
 178         mv -f ${dir} ${productionDir}
 179       done
 180
 181       echo running ${detector} periodLevelQA for production ${period}/${pass}
 182       rm -f trending.root
 183
 184       #merge trending files if any
 185       if /bin/ls 000*/trending.root &>/dev/null; then
 186         hadd trending.root 000*/trending.root &> periodLevelQA.log
 187         periodLevelQA trending.root &>> periodLevelQA.log
 188       fi
 189
 190       if ! validate ${PWD}; then continue; fi
 191
 192       cd ${tmpDetectorRunDir}
 193
 194     done
 195
 196     cd ${workingDirectory}
 197
 198     if [[ -z ${planB} ]]; then
 199       echo
 200       echo removing ${tmpDetectorRunDir}
 201       rm -rf ${tmpDetectorRunDir}
 202     else
 203       executePlanB
 204     fi
 205   done
 206
 207   #remove lock
 208   rm -f ${lockFile}
 209 }
 210
 211 executePlanB()
 212 {
 213   #in case of emergency
 214   if [[ -n ${MAILTO} ]]; then
 215     echo
 216     echo "trouble detected, sending email to ${MAILTO}"
 217
 218     cat ${logSummary} | mail -s "qa in need of assistance" ${MAILTO}
 219   fi
 220 }
 221
 222 validate()
 223 {
 224   summarizeLogs ${1} >> ${logSummary}
 225   logStatus=$?
 226   if [[ ${logStatus} -ne 0 ]]; then
 227     echo "WARNING not validated: ${1}"
 228     planB=1
 229     return 1
 230   fi
 231   return 0
 232 }
 233
 234 summarizeLogs()
 235 {
 236   local dir=$1
 237   [[ ! -d ${dir} ]] && dir=${PWD}
 238
 239   #print a summary of logs
 240   logFiles=(
 241       "*.log"
 242       "stdout"
 243       "stderr"
 244   )
 245
 246   #check logs
 247   local logstatus=0
 248   for log in ${dir}/${logFiles[*]}; do
 249     finallog=${PWD%/}/${log}
 250     [[ ! -f ${log} ]] && continue
 251     errorSummary=$(validateLog ${log})
 252     validationStatus=$?
 253     [[ validationStatus -ne 0 ]] && logstatus=1
 254     if [[ ${validationStatus} -eq 0 ]]; then
 255       #in pretend mode randomly report an error in rec.log some cases
 256       if [[ -n ${pretend} && "${log}" == "rec.log" ]]; then
 257         [[ $(( ${RANDOM}%2 )) -ge 1 ]] && echo "${finallog} BAD random error" || echo "${finallog} OK"
 258       else
 259         echo "${finallog} OK"
 260       fi
 261     elif [[ ${validationStatus} -eq 1 ]]; then
 262       echo "${finallog} BAD ${errorSummary}"
 263     elif [[ ${validationStatus} -eq 2 ]]; then
 264       echo "${finallog} OK MWAH ${errorSummary}"
 265     fi
 266   done
 267
 268   #report core files
 269   while read x; do
 270     echo ${x}
 271     chmod 644 ${x}
 272     gdb --batch --quiet -ex "bt" -ex "quit" aliroot ${x} > stacktrace_${x//\//_}.log
 273   done < <(/bin/ls ${PWD}/*/core 2>/dev/null; /bin/ls ${PWD}/core 2>/dev/null)
 274
 275   return ${logstatus}
 276 }
 277
 278 validateLog()
 279 {
 280   log=${1}
 281   errorConditions=(
 282             'There was a crash'
 283             'floating'
 284             'error while loading shared libraries'
 285             'std::bad_alloc'
 286             's_err_syswatch_'
 287             'Thread [0-9]* (Thread'
 288             'AliFatal'
 289             'core dumped'
 290             '\.C.*error:.*\.h: No such file'
 291             'segmentation'
 292   )
 293
 294   warningConditions=(
 295             'This is serious'
 296   )
 297
 298   local logstatus=0
 299   local errorSummary=""
 300   local warningSummary=""
 301
 302   for ((i=0; i<${#errorConditions[@]};i++)); do
 303     local tmp=$(grep -m1 -e "${errorConditions[${i}]}" ${log})
 304     [[ -n ${tmp} ]] && tmp+=" : "
 305     errorSummary+=${tmp}
 306   done
 307
 308   for ((i=0; i<${#warningConditions[@]};i++)); do
 309     local tmp=$(grep -m1 -e "${warningConditions[${i}]}" ${log})
 310     [[ -n ${tmp} ]] && tmp+=" : "
 311     warningSummary+=${tmp}
 312   done
 313
 314   if [[ -n ${errorSummary} ]]; then
 315     echo "${errorSummary}"
 316     return 1
 317   fi
 318
 319   if [[ -n ${warningSummary} ]]; then
 320     echo "${warningSummary}"
 321     return 2
 322   fi
 323
 324   return 0
 325 }
 326
 327 parseConfig()
 328 {
 329   #config file
 330   configFile=""
 331   #where to search for qa files
 332   inputList=file.list
 333   #working directory
 334   workingDirectory="${PWD}"
 335   #where to place the final qa plots
 336   #outputDirectory="/afs/cern.ch/work/a/aliqa%det/www/"
 337   outputDirectory="${workingDirectory}/%DET"
 338   #filter out detector option
 339   excludeDetectors="EXAMPLE"
 340   #logs
 341   logDirectory=${workingDirectory}/logs
 342   #set aliroot
 343   #alirootEnv="/home/mkrzewic/alisoft/balice_master.sh"
 344   #OCDB storage
 345   #ocdbStorage="raw://"
 346   #email to
 347   #MAILTO="fbellini@cern.ch"
 348
 349   #first, check if the config file is configured
 350   #is yes - source it so that other options can override it
 351   #if any
 352   for opt in $@; do
 353     if [[ ${opt} =~ configFile=.* ]]; then
 354       eval "${opt}"
 355       [[ ! -f ${configFile} ]] && echo "configFile ${configFile} not found, exiting..." && return 1
 356       source "${configFile}"
 357       break
 358     fi
 359   done
 360
 361   #then, parse the options as they override the options from file
 362   while [[ -n ${1} ]]; do
 363     local var=${1#--}
 364     if [[ ${var} =~ .*=.* ]]; then
 365       eval "${var}"
 366     else
 367       echo "badly formatted option ${var}, should be: option=value, stopping..."
 368       return 1
 369     fi
 370     shift
 371   done
 372 }
 373
 374 guessRunData()
 375 {
 376   #guess the period from the path, pick the rightmost one
 377   period=""
 378   runNumber=""
 379   year=""
 380   pass=""
 381   legoTrainRunNumber=""
 382   dataType=""
 383
 384   local shortRunNumber=""
 385   local IFS="/"
 386   declare -a path=( $1 )
 387   local dirDepth=$(( ${#path[*]}-1 ))
 388   i=0
 389   for ((x=${dirDepth};x>=0;x--)); do
 390
 391     [[ $((x-1)) -ge 0 ]] && local fieldPrev=${path[$((x-1))]}
 392     local field=${path[${x}]}
 393     local fieldNext=${path[$((x+1))]}
 394
 395     [[ ${field} =~ ^[0-9]*$ && ${fieldNext} =~ (.*\.zip$|.*\.root$) ]] && legoTrainRunNumber=${field}
 396     [[ -n ${legoTrainRunNumber} && -z ${pass} ]] && pass=${fieldPrev}
 397     [[ ${field} =~ ^LHC[0-9][0-9][a-z].*$ ]] && period=${field%_*}
 398     [[ ${field} =~ ^000[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && runNumber=${field#000}
 399     [[ ${field} =~ ^[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && shortRunNumber=${field}
 400     [[ ${field} =~ ^20[0-9][0-9]$ ]] && year=${field}
 401     [[ ${field} =~ ^(^sim$|^data$) ]] && dataType=${field}
 402     (( i++ ))
 403   done
 404   [[ -z ${legoTrainRunNumber} ]] && pass=${path[$((dirDepth-1))]}
 405   [[ "${dataType}" =~ ^sim$ ]] && pass="passMC" && runNumber=${shortRunNumber}
 406
 407   #if [[ -z ${dataType} || -z ${year} || -z ${period} || -z ${runNumber}} || -z ${pass} ]];
 408   if [[ -z ${runNumber}} ]];
 409   then
 410     #error condition
 411     return 1
 412   else
 413     #ALL OK
 414     return 0
 415   fi
 416 }
 417
 418 substituteDetectorName()
 419 {
 420   local det=$1
 421   local dir=$2
 422   [[ ${dir} =~ \%det ]] && det=${det,,} && echo ${dir/\%det/${det}}
 423   [[ ${dir} =~ \%DET ]] && det=${det} && echo ${dir/\%DET/${det}}
 424 }
 425
 426 get_realpath()
 427 {
 428   if [[ -f "$1" ]]
 429   then
 430     # file *must* exist
 431     if cd "$(echo "${1%/*}")" &>/dev/null
 432     then
 433       # file *may* not be local
 434       # exception is ./file.ext
 435       # try 'cd .; cd -;' *works!*
 436       local tmppwd="$PWD"
 437       cd - &>/dev/null
 438     else
 439       # file *must* be local
 440       local tmppwd="$PWD"
 441     fi
 442   else
 443     # file *cannot* exist
 444     return 1 # failure
 445   fi
 446   # reassemble realpath
 447   echo "$tmppwd"/"${1##*/}"
 448   return 0 # success
 449 }
 450
 451 main $@