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 ${alienUserName}
  24     #this is a hack! alien-token init seems not enough
  25     #but the gclient_env script messes up the LD_LIBRARY_PATH
  26     while read x; do
  27       eval ${x};
  28     done < <(grep -v "LD_LIBRARY_PATH" /tmp/gclient_env_${UID})
  29   fi
  30
  31   updateQA "$@"
  32 }
  33
  34 updateQA()
  35 {
  36   umask 0002
  37   parseConfig "$@"
  38
  39   #be paranoid and make some full paths
  40   [[ ! -f ${inputList} ]] && echo "no input list: ${inputList}" && return 1
  41   inputList=$(get_realpath ${inputList})
  42   mkdir -p ${workingDirectory}
  43   workingDirectory=$(workingDirectory=${workingDirectory%/}; cd ${workingDirectory%/*}; echo "${PWD}/${workingDirectory##*/}")
  44   if [[ ! -d ${workingDirectory} ]]; then
  45     echo "working dir $workingDirectory does not exist and cannot be created"
  46     return 1
  47   fi
  48   cd ${workingDirectory}
  49
  50   echo JOB config:
  51   echo inputList=$inputList
  52   echo outputDirectory=$outputDirectory
  53   echo
  54
  55   dateString=$(date +%Y-%m-%d-%H-%M)
  56   echo "Start time QA process: $dateString"
  57
  58   #logging
  59   mkdir -p $logDirectory
  60   [[ ! -d $logDirectory ]] && echo "no log dir $logDirectory" && return 1
  61   logFile="$logDirectory/${0##*/}.${dateString}.log"
  62   touch ${logFile}
  63   [[ ! -f ${logFile} ]] && echo "cannot write logfile $logfile" && return 1
  64   echo "logFile = $logFile"
  65
  66   #check lock
  67   lockFile=${logDirectory}/runQA.lock
  68   [[ -f ${lockFile} ]] && echo "lock ${lockFile} exists!" | tee ${logFile} && return 1
  69   touch ${lockFile}
  70   [[ ! -f ${lockFile} ]] && echo "cannot lock $lockFile" | tee ${logFile} && return 1
  71
  72   exec &>${logFile}
  73
  74   ################################################################
  75   #ze detector loop
  76   for detectorScript in $ALICE_ROOT/PWGPP/QA/detectorQAscripts/*; do
  77     echo
  78     echo "##############################################"
  79     echo $(date)
  80     unset planB
  81     [[ ! ${detectorScript} =~ .*\.sh$ ]] && continue
  82     detector=${detectorScript%.sh}
  83     detector=${detector##*/}
  84
  85     #skip if excluded
  86     if [[ "${excludeDetectors}" =~ ${detector} ]]; then
  87       echo "${detector} is excluded in config, skipping..."
  88       continue
  89     fi
  90
  91     #if includeDetectors set, only process thoe detectors specified there
  92     if [[ -n ${includeDetectors} && ! "${includeDetectors}" =~ ${detector} ]]; then
  93       echo "${detector} not included in includeDetectors, skipping..."
  94       continue
  95     fi
  96
  97     logSummary=${logDirectory}/summary-${detector}-${dateString}.log
  98     outputDir=$(substituteDetectorName ${detector} ${outputDirectory})
  99     tmpDetectorRunDir=${workingDirectory}/tmpQAtmpRunDir${detector}-${dateString}
 100     if ! mkdir -p ${tmpDetectorRunDir}; then
 101       echo "cannot create the temp dir $tmpDetectorRunDir"
 102       continue
 103     fi
 104     cd ${tmpDetectorRunDir}
 105
 106     tmpPrefix=${tmpDetectorRunDir}/${outputDir}
 107     echo "running QA for ${detector}"
 108     echo "  outputDir=$outputDir"
 109     echo "  tmpPrefix=$tmpPrefix"
 110
 111     #unset the detector functions from previous iterations (detectors)
 112     unset -f runLevelQA
 113     unset -f periodLevelQA
 114     unset -f runLevelHighPtTreeQA
 115     unset -f periodLevelHighPtTreeQA
 116     source ${detectorScript}
 117
 118     #################################################################
 119     #produce the QA and trending tree for each file (run)
 120     unset arrOfTouchedProductions
 121     declare -A arrOfTouchedProductions
 122     while read qaFile; do
 123       echo
 124       echo $(date)
 125
 126       #first check if input file exists
 127       [[ ! -f ${qaFile%\#*} ]] && echo "file ${qaFile%\#*} not accessible" && continue
 128
 129       if ! guessRunData ${qaFile}; then
 130         echo "could not guess run data from ${qaFile}"
 131         continue
 132       fi
 133
 134       tmpProductionDir=${tmpPrefix}/${dataType}/${year}/${period}/${pass}
 135       tmpRunDir=${tmpProductionDir}/000${runNumber}
 136       mkdir -p ${tmpRunDir}
 137       cd ${tmpRunDir}
 138
 139       #by default we expect to have everything in the same archive
 140       highPtTree=${qaFile}
 141
 142       #maybe the input is not an archive, but a file
 143       [[ "${qaFile}" =~ QAresults.root$ ]] && highPtTree=""
 144       [[ "${qaFile}" =~ FilterEvents_Trees.root$ ]] && qaFile=""
 145
 146       #it is possible we get the highPt trees from somewhere else
 147       #search the list of high pt trees for the proper run number
 148       if [[ -n ${inputListHighPtTrees} ]]; then
 149         highPtTree=$(egrep -m1 ${runNumber} ${inputListHighPtTrees})
 150         echo "loaded the highPtTree ${highPtTree} from external file ${inputListHighPtTrees}"
 151       fi
 152
 153       echo qaFile=$qaFile
 154       echo highPtTree=$highPtTree
 155       echo ocdbStorage=${ocdbStorage}
 156       echo
 157
 158       #what if we have a zip archive?
 159       if [[ "$qaFile" =~ .*.zip$ ]]; then
 160         if unzip -l ${qaFile} | egrep "QAresults.root" &>/dev/null; then
 161           qaFile="${qaFile}#QAresults.root"
 162         else
 163           qaFile=""
 164         fi
 165       fi
 166       if [[ "$highPtTree" =~ .*.zip$ ]]; then
 167         if unzip -l ${highPtTree} | egrep "FilterEvents_Trees.root" &>/dev/null; then
 168           highPtTree="${highPtTree}#FilterEvents_Trees.root"
 169         else
 170           highPtTree=""
 171         fi
 172       fi
 173
 174       if [[ -n ${qaFile} && $(type -t runLevelQA) =~ "function" ]]; then
 175         echo running ${detector} runLevelQA for run ${runNumber} from ${qaFile}
 176         runLevelQA "${qaFile}" &> runLevelQA.log
 177         #perform some default actions:
 178         #if trending.root not created, create a default one
 179         if [[ ! -f trending.root ]]; then
 180           aliroot -b -q -l "$ALICE_ROOT/PWGPP/macros/simpleTrending.C(\"${qaFile}\",${runNumber},\"${detector}\",\"trending.root\",\"trending\",\"recreate\")" 2>&1 | tee -a runLevelQA.log
 181         fi
 182         if [[ -f trending.root ]]; then
 183           arrOfTouchedProductions[${tmpProductionDir}]=1
 184         else
 185           echo "trending.root not created"
 186         fi
 187       fi
 188       #expert QA based on high pt trees
 189       if [[ -n ${highPtTree} && $(type -t runLevelHighPtTreeQA) =~ "function" ]]; then
 190         echo running ${detector} runLevelHighPtTreeQA for run ${runNumber} from ${highPtTree}
 191         runLevelHighPtTreeQA "${highPtTree}" &> runLevelHighPtTreeQA.log
 192         arrOfTouchedProductions[${tmpProductionDir}]=1
 193       fi
 194
 195       cd ${tmpDetectorRunDir}
 196
 197     done < ${inputList}
 198
 199     #################################################################
 200     #cache which productions were (re)done
 201     echo "list of processed productions:"
 202     echo "    ${!arrOfTouchedProductions[@]}"
 203     echo
 204
 205     #################################################################
 206     #(re)do the merging/trending
 207     for tmpProductionDir in ${!arrOfTouchedProductions[@]}; do
 208       cd ${tmpProductionDir}
 209       echo
 210       echo "running period level stuff in ${tmpProductionDir}"
 211       echo $(date)
 212
 213       productionDir=${outputDir}/${tmpProductionDir#${tmpPrefix}}
 214       echo productionDir=${outputDir}/${tmpProductionDir#${tmpPrefix}}
 215
 216       mkdir -p ${productionDir}
 217       if [[ ! -d ${productionDir} ]]; then
 218         echo "cannot make productionDir $productionDir" && continue
 219       fi
 220
 221       #move runs to final destination
 222       for dir in ${tmpProductionDir}/000*; do
 223         echo
 224         oldRunDir=${outputDir}/${dir#${tmpPrefix}}
 225         if ! guessRunData "${dir}/dummyName"; then
 226           echo "could not guess run data from ${dir}"
 227           continue
 228         fi
 229
 230         #before moving - VALIDATE!!!
 231         if ! validate ${dir}; then
 232           continue
 233         fi
 234
 235         #moving a dir is an atomic operation, no locking necessary
 236         if [[ -d ${oldRunDir} ]]; then
 237           echo "removing old ${oldRunDir}"
 238           rm -rf ${oldRunDir}
 239         fi
 240         echo "moving new ${runNumber} to ${productionDir}"
 241         mv -f ${dir} ${productionDir}
 242       done
 243
 244       #go to a temp dir to do the period level stuff in a completely clean dir
 245       tmpPeriodLevelQAdir="${tmpProductionDir}/periodLevelQA"
 246       echo
 247       echo tmpPeriodLevelQAdir="${tmpProductionDir}/periodLevelQA"
 248       if ! mkdir -p ${tmpPeriodLevelQAdir}; then continue; fi
 249       cd ${tmpPeriodLevelQAdir}
 250
 251       #link the final list of per-run dirs here, just the dirs
 252       #to have a clean working directory
 253       unset linkedStuff
 254       declare -a linkedStuff
 255       for x in ${productionDir}/000*; do [[ -d $x ]] && ln -s $x && linkedStuff+=(${x##*/}); done
 256
 257       #merge trending files if any
 258       if /bin/ls 000*/trending.root &>/dev/null; then
 259         hadd trending.root 000*/trending.root &> periodLevelQA.log
 260       fi
 261
 262       #run the period level trending/QA
 263       if [[ -f "trending.root" && $(type -t periodLevelQA) =~ "function" ]]; then
 264         echo running ${detector} periodLevelQA for production ${period}/${pass}
 265         periodLevelQA trending.root &>> periodLevelQA.log
 266       else
 267         echo "WARNING: not running ${detector} periodLevelQA for production ${period}/${pass}, no trending.root"
 268       fi
 269
 270       if ! validate ${PWD}; then continue; fi
 271
 272       #here we are validated so move the produced QA to the final place
 273       #clean up linked stuff first
 274       [[ -n ${linkedStuff[@]} ]] && rm ${linkedStuff[@]}
 275       periodLevelLock=${productionDir}/runQA.lock
 276       if [[ ! -f ${periodLevelLock} ]]; then
 277         #some of the output could be a directory, so handle that
 278         #TODO: maybe use rsync?
 279         #lock to avoid conflicts:
 280         echo "${HOSTNAME} ${dateString}" > ${periodLevelLock}
 281         for x in ${tmpPeriodLevelQAdir}/*; do
 282           if [[ -d ${x} ]]; then
 283             echo "removing ${productionDir}/${x##*/}"
 284             rm -rf ${productionDir}/${x##*/}
 285             echo "moving ${x} to ${productionDir}"
 286             mv ${x} ${productionDir}
 287           fi
 288           if [[ -f ${x} ]]; then
 289             echo "moving ${x} to ${productionDir}"
 290             mv -f ${x} ${productionDir}
 291           fi
 292         done
 293         rm -f ${periodLevelLock}
 294         #remove the temp dir
 295         rm -rf ${tmpPeriodLevelQAdir}
 296       else
 297         echo "ERROR: cannot move to destination"                     >> ${logSummary}
 298         echo "production dir ${productionDir} locked!"               >> ${logSummary}
 299         echo "check and maybe manually do:"                          >> ${logSummary}
 300         echo " rm ${periodLevelLock}"                                >> ${logSummary}
 301         echo " rsync -av ${tmpPeriodLevelQAdir}/ ${productionDir}/"  >> ${logSummary}
 302         planB=1
 303       fi
 304
 305     done
 306
 307     cd ${workingDirectory}
 308
 309     if [[ -z ${planB} ]]; then
 310       echo
 311       echo removing ${tmpDetectorRunDir}
 312       rm -rf ${tmpDetectorRunDir}
 313     else
 314       executePlanB
 315     fi
 316   done #end of detector loop
 317
 318   #remove lock
 319   rm -f ${lockFile}
 320 }
 321
 322 executePlanB()
 323 {
 324   #in case of emergency
 325   if [[ -n ${MAILTO} ]]; then
 326     echo
 327     echo "trouble detected, sending email to ${MAILTO}"
 328
 329     grep BAD ${logSummary} | mail -s "qa in need of assistance" ${MAILTO}
 330   fi
 331 }
 332
 333 validate()
 334 {
 335   summarizeLogs ${1} >> ${logSummary}
 336   logStatus=$?
 337   if [[ ${logStatus} -ne 0 ]]; then
 338     echo "WARNING not validated: ${1}"
 339     planB=1
 340     return 1
 341   fi
 342   return 0
 343 }
 344
 345 summarizeLogs()
 346 {
 347   local dir=$1
 348   [[ ! -d ${dir} ]] && dir=${PWD}
 349
 350   #print a summary of logs
 351   logFiles=(
 352       "*.log"
 353       "stdout"
 354       "stderr"
 355   )
 356
 357   #check logs
 358   local logstatus=0
 359   for log in ${dir}/${logFiles[*]}; do
 360     finallog=${PWD%/}/${log}
 361     [[ ! -f ${log} ]] && continue
 362     errorSummary=$(validateLog ${log})
 363     validationStatus=$?
 364     [[ validationStatus -ne 0 ]] && logstatus=1
 365     if [[ ${validationStatus} -eq 0 ]]; then
 366       #in pretend mode randomly report an error in rec.log some cases
 367       if [[ -n ${pretend} && "${log}" == "rec.log" ]]; then
 368         [[ $(( ${RANDOM}%2 )) -ge 1 ]] && echo "${finallog} BAD random error" || echo "${finallog} OK"
 369       else
 370         echo "${finallog} OK"
 371       fi
 372     elif [[ ${validationStatus} -eq 1 ]]; then
 373       echo "${finallog} BAD ${errorSummary}"
 374     elif [[ ${validationStatus} -eq 2 ]]; then
 375       echo "${finallog} OK MWAH ${errorSummary}"
 376     fi
 377   done
 378
 379   #report core files
 380   while read x; do
 381     echo ${x}
 382     chmod 644 ${x}
 383     gdb --batch --quiet -ex "bt" -ex "quit" aliroot ${x} > stacktrace_${x//\//_}.log
 384   done < <(/bin/ls ${PWD}/*/core 2>/dev/null; /bin/ls ${PWD}/core 2>/dev/null)
 385
 386   return ${logstatus}
 387 }
 388
 389 validateLog()
 390 {
 391   log=${1}
 392   errorConditions=(
 393             'There was a crash'
 394             'floating'
 395             'error while loading shared libraries'
 396             'std::bad_alloc'
 397             's_err_syswatch_'
 398             'Thread [0-9]* (Thread'
 399             'AliFatal'
 400             'core dumped'
 401             '\.C.*error:.*\.h: No such file'
 402             'segmentation'
 403             'Interpreter error recovered'
 404   )
 405
 406   warningConditions=(
 407             'This is serious'
 408   )
 409
 410   local logstatus=0
 411   local errorSummary=""
 412   local warningSummary=""
 413
 414   for ((i=0; i<${#errorConditions[@]};i++)); do
 415     local tmp=$(grep -m1 -e "${errorConditions[${i}]}" ${log})
 416     [[ -n ${tmp} ]] && tmp+=" : "
 417     errorSummary+=${tmp}
 418   done
 419
 420   for ((i=0; i<${#warningConditions[@]};i++)); do
 421     local tmp=$(grep -m1 -e "${warningConditions[${i}]}" ${log})
 422     [[ -n ${tmp} ]] && tmp+=" : "
 423     warningSummary+=${tmp}
 424   done
 425
 426   if [[ -n ${errorSummary} ]]; then
 427     echo "${errorSummary}"
 428     return 1
 429   fi
 430
 431   if [[ -n ${warningSummary} ]]; then
 432     echo "${warningSummary}"
 433     return 2
 434   fi
 435
 436   return 0
 437 }
 438
 439 parseConfig()
 440 {
 441   args=("$@")
 442
 443   #config file
 444   configFile=""
 445   #where to search for qa files
 446   inputList=file.list
 447   #working directory
 448   workingDirectory="${PWD}"
 449   #where to place the final qa plots
 450   #outputDirectory="/afs/cern.ch/work/a/aliqa%det/www/"
 451   outputDirectory="${workingDirectory}/%DET"
 452   #filter out detector option
 453   excludeDetectors="EXAMPLE"
 454   #logs
 455   logDirectory=${workingDirectory}/logs
 456   #OCDB storage
 457   ocdbStorage="raw://"
 458   #email to
 459   #MAILTO="fbellini@cern.ch"
 460
 461   #first, check if the config file is configured
 462   #is yes - source it so that other options can override it
 463   #if any
 464   for opt in "${args[@]}"; do
 465     if [[ ${opt} =~ configFile=.* ]]; then
 466       eval "${opt}"
 467       [[ ! -f ${configFile} ]] && echo "configFile ${configFile} not found, exiting..." && return 1
 468       echo "using config file: ${configFile}"
 469       source "${configFile}"
 470       break
 471     fi
 472   done
 473
 474   #then, parse the options as they override the options from file
 475   for opt in "${args[@]}"; do
 476     if [[ ! "${opt}" =~ .*=.* ]]; then
 477       echo "badly formatted option ${var}, should be: option=value, stopping..."
 478       return 1
 479     fi
 480     local var="${opt%%=*}"
 481     local value="${opt#*=}"
 482     echo "${var}=${value}"
 483     export ${var}="${value}"
 484   done
 485 }
 486
 487 guessRunData()
 488 {
 489   #guess the period from the path, pick the rightmost one
 490   period=""
 491   runNumber=""
 492   year=""
 493   pass=""
 494   legoTrainRunNumber=""
 495   dataType=""
 496
 497   local shortRunNumber=""
 498   oldIFS=${IFS}
 499   local IFS="/"
 500   declare -a path=( $1 )
 501   IFS="${oldIFS}"
 502   local dirDepth=$(( ${#path[*]}-1 ))
 503   i=0
 504   for ((x=${dirDepth};x>=0;x--)); do
 505
 506     [[ $((x-1)) -ge 0 ]] && local fieldPrev=${path[$((x-1))]}
 507     local field=${path[${x}]}
 508     local fieldNext=${path[$((x+1))]}
 509
 510     [[ ${field} =~ ^[0-9]*$ && ${fieldNext} =~ (.*\.zip$|.*\.root$) ]] && legoTrainRunNumber=${field}
 511     [[ -n ${legoTrainRunNumber} && -z ${pass} ]] && pass=${fieldPrev}
 512     [[ ${field} =~ ^LHC[0-9][0-9][a-z].*$ ]] && period=${field%_*}
 513     [[ ${field} =~ ^000[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && runNumber=${field#000}
 514     [[ ${field} =~ ^[0-9][0-9][0-9][0-9][0-9][0-9]$ ]] && shortRunNumber=${field}
 515     [[ ${field} =~ ^20[0-9][0-9]$ ]] && year=${field}
 516     [[ ${field} =~ ^(^sim$|^data$) ]] && dataType=${field}
 517     (( i++ ))
 518   done
 519   [[ -z ${legoTrainRunNumber} ]] && pass=${path[$((dirDepth-1))]}
 520   [[ "${dataType}" =~ ^sim$ ]] && pass="passMC" && runNumber=${shortRunNumber}
 521   [[ -n ${legoTrainRunNumber} ]] && pass+="_lego${legoTrainRunNumber}"
 522
 523   #modify the OCDB: set the year
 524   ocdbStorage=$(setYear ${year} ${ocdbStorage})
 525
 526   #if [[ -z ${dataType} || -z ${year} || -z ${period} || -z ${runNumber}} || -z ${pass} ]];
 527   if [[ -z ${runNumber}} ]]
 528   then
 529     #error condition
 530     return 1
 531   else
 532     #ALL OK
 533     return 0
 534   fi
 535 }
 536
 537 substituteDetectorName()
 538 {
 539   local det=$1
 540   local dir=$2
 541   [[ ${dir} =~ \%det ]] && det=${det,,} && echo ${dir/\%det/${det}}
 542   [[ ${dir} =~ \%DET ]] && det=${det} && echo ${dir/\%DET/${det}}
 543 }
 544
 545 get_realpath()
 546 {
 547   if [[ -f "$1" ]]
 548   then
 549     # file *must* exist
 550     if cd "$(echo "${1%/*}")" &>/dev/null
 551     then
 552       # file *may* not be local
 553       # exception is ./file.ext
 554       # try 'cd .; cd -;' *works!*
 555       local tmppwd="$PWD"
 556       cd - &>/dev/null
 557     else
 558       # file *must* be local
 559       local tmppwd="$PWD"
 560     fi
 561   else
 562     # file *cannot* exist
 563     return 1 # failure
 564   fi
 565   # reassemble realpath
 566   echo "$tmppwd"/"${1##*/}"
 567   return 0 # success
 568 }
 569
 570 setYear()
 571 {
 572   #set the year
 573   #  ${1} - year to be set
 574   #  ${2} - where to set the year
 575   local year1=$(guessYear ${1})
 576   local year2=$(guessYear ${2})
 577   local path=${2}
 578   [[ ${year1} -ne ${year2} && -n ${year2} && -n ${year1} ]] && path=${2/\/${year2}\//\/${year1}\/}
 579   echo ${path}
 580   return 0
 581 }
 582
 583 guessYear()
 584 {
 585   #guess the year from the path, pick the rightmost one
 586   local IFS="/"
 587   declare -a pathArray=( ${1} )
 588   local field
 589   local year
 590   for field in ${pathArray[@]}; do
 591     [[ ${field} =~ ^20[0-9][0-9]$ ]] && year=${field}
 592   done
 593   echo ${year}
 594   return 0
 595 }
 596
 597 main "$@"