+#!/usr/bin/env bash
#library of useful PWGPP related bash functions
#it REQUIRES BASH 4 !!!!
#blame: Mikolaj Krzewicki, mkrzewic@cern.ch
2010 108350 139517
2011 140441 170593
2012 171590 193766
-2013 194482 197692
-2014 197693 999999
+2013 194308 199146
+2014 202369 206695
+2015 999999 999999
+2016 999999 999999
"
parseConfig()
{
- local args=("$@")
-
- #first, check if the config file is configured
- #is yes - source it so that other options can override it
+ #parse command line arguments, they have to be in the form
+ # option=value
+ #they are then set in the environment
+ #
+ #optionally a config file can be specified in the arguments:
+ # configFile=<someFile>
+ #config file sets variables: option=value
+ #command line options override config file
#
#recommended way of using (at the beginning of your funcion/script):
# if ! parseConfig "${@}"; then return; fi
+ local args=("$@")
local opt=""
#first check if we will need to decode spaces
guessRunData()
{
#guess the period from the path, pick the rightmost one
+ #if $ocdbStorage is set it will be reset to the anchorYear (for MC)
period=""
runNumber=""
year=""
local oldIFS=${IFS}
local IFS="/"
+ [[ -z ${1} ]] && return 1
declare -a path=( $1 )
IFS="${oldIFS}"
local dirDepth=$(( ${#path[*]}-1 ))
[[ ${field} =~ ^20[0-9][0-9]$ ]] && year=${field}
[[ ${field} =~ ^(^sim$|^data$) ]] && dataType=${field}
done
-
originalPass=${pass}
- [[ -n ${shortRunNumber} && "${legoTrainRunNumber}" =~ ${shortRunNumber} ]] && legoTrainRunNumber=""
- [[ -z ${legoTrainRunNumber} ]] && pass=${path[$((dirDepth-1))]}
- [[ "${dataType}" =~ ^sim$ ]] && pass="passMC" && runNumber=${shortRunNumber} && originalPass="" #for MC not from lego, the runnumber is identified as lego train number, thus needs to be nulled
- [[ -n ${legoTrainRunNumber} ]] && pass+="_lego${legoTrainRunNumber}"
-
- #modify the OCDB: set the year
- if [[ ${dataType} =~ sim ]]; then
+
+ if [[ ${dataType} =~ sim ]]; then
+ [[ -n ${shortRunNumber} && -z ${runNumber} ]] && runNumber=${shortRunNumber}
+ pass="passMC"
+ originalPass="" #for MC not from lego, the runNumber is identified as lego train number, thus needs to be nulled
anchorYear=$(run2year $runNumber)
if [[ -z "${anchorYear}" ]]; then
echo "WARNING: anchorYear not available for this production: ${originalPeriod}, runNumber: ${runNumber}. Cannot set the OCDB."
return 1
fi
+ #modify the OCDB: set the year
ocdbStorage=$(setYear ${anchorYear} ${ocdbStorage})
else
ocdbStorage=$(setYear ${year} ${ocdbStorage})
fi
+ [[ -n ${shortRunNumber} && -z ${runNumber} && -z {dataType} ]] && runNumber=${shortRunNumber}
+ [[ -n ${shortRunNumber} && "${legoTrainRunNumber}" =~ ${shortRunNumber} ]] && legoTrainRunNumber=""
+ [[ -z ${legoTrainRunNumber} && ${dataType} == "data" ]] && pass=${path[$((dirDepth-1))]}
+ [[ -n ${legoTrainRunNumber} ]] && pass+="_lego${legoTrainRunNumber}"
+
#if [[ -z ${dataType} || -z ${year} || -z ${period} || -z ${runNumber}} || -z ${pass} ]];
if [[ -z ${runNumber} ]]
then
return 0
}
+guessRunNumber()
+(
+ #guess the run number from the path, pick the rightmost one
+ if guessRunData "${1}"; then
+ echo ${runNumber}
+ return 0
+ fi
+ return 1
+)
+
+guessYear()
+(
+ #guess the year from the path, pick the rightmost one
+ if guessRunData "${1}"; then
+ echo ${year}
+ return 0
+ fi
+ return 1
+)
+
+guessPeriod()
+(
+ #guess the period from the path, pick the rightmost one
+ if guessRunData "${1}"; then
+ echo ${period}
+ return 0
+ fi
+ return 1
+)
+
setYear()
{
- #set the year
+ #set the year in the string
+ #usualy used to modify the year in $ocdbStorage
# ${1} - year to be set
# ${2} - where to set the year
- local year1=$(guessYear ${1})
- local year2=$(guessYear ${2})
+ #if AUTOYEAR is present in target - it will be replaced by the year
+ local yearSource=$(guessYearFast ${1})
+ local yearTarget=$(guessYearFast ${2})
local path=${2}
- [[ ${year1} -ne ${year2} && -n ${year2} && -n ${year1} ]] && path=${2/\/${year2}\//\/${year1}\/}
- echo ${path}
+ [[ ${yearSource} -ne ${yearTarget} && -n ${yearTarget} && -n ${yearSource} ]] \
+ && path=${2/\/"${yearTarget}"/\/"${yearSource}"}
+ path=${path/\/\//\/}
+ # The previous line would transform raw:// in raw:/
+ # The next fixes this
+ echo ${path/%:\//:\/\/}
return 0
}
-guessYear()
+guessYearFast()
{
#guess the year from the path, pick the rightmost one
+ #is string AUTOYEAR present, will be returned
local IFS="/"
declare -a pathArray=( ${1} )
- local field
- local year
+ local field=""
+ local year=""
+ local autoYear=""
for field in ${pathArray[@]}; do
- [[ ${field} =~ ^20[0-9][0-9]$ ]] && year=${field}
+ [[ ${field} =~ ^20[0-9][0-9]$ ]] && year="${field}"
+ [[ ${field} == AUTOYEAR ]] && autoYear="${field}"
done
+ [[ -n ${autoYear} ]] && year="${autoYear}"
echo ${year}
return 0
}
#input is a list of logs, or a glob:
#example (summarizes logs in current and subdirs):
# summarizeLogs * */*
+ #if no args given, process all files in PWD
#exit code 1 if some logs are not validated
#print a summary of logs
#double inclusion protection+make full paths
for file in "${input[@]}"; do
- [[ ! "${file}" =~ ^/ ]] && file="${PWD}"/"${file}"
+ [[ ! "${file}" =~ ^/ ]] && file="${PWD}/${file}"
files["${file}"]="${file}"
done
local logFiles
- logFiles=".*log|stdout|stderr"
+ logFiles="\.*log$|^stdout$|^stderr$"
#check logs
local logStatus=0
for file in "${files[@]}"; do
[[ ! -f ${file} ]] && continue
#keep track of core files for later processing
- [[ "${file}" =~ core$ ]] && coreFiles[${file}]="${file}" && continue
- [[ ! "${file}" =~ ${logFiles} ]] && continue
+ [[ "${file##*/}" =~ ^core$ ]] && coreFiles[${file}]="${file}" && continue
+ [[ ! "${file##*/}" =~ ${logFiles} ]] && continue
errorSummary=$(validateLog ${file})
validationStatus=$?
[[ validationStatus -ne 0 ]] && logStatus=1
for x in "${coreFiles[@]}"; do
echo ${x}
chmod 644 ${x}
- gdb --batch --quiet -ex "bt" -ex "quit" aliroot ${x} > stacktrace_${x//\//_}.log
+ #gdb --batch --quiet -ex "bt" -ex "quit" aliroot ${x} > stacktrace_${x//\//_}.log
+ gdb --batch --quiet -ex "bt" -ex "quit" aliroot ${x} > stacktrace.log
local nLines[2]
- nLines=($(wc -l stacktrace_${x//\//_}.log))
+ #nLines=($(wc -l stacktrace_${x//\//_}.log))
+ nLines=($(wc -l stacktrace.log))
if [[ ${nLines[0]} -eq 0 ]]; then
- rm stacktrace_${x//\//_}.log
+ #rm stacktrace_${x//\//_}.log
+ rm stacktrace.log
else
logStatus=1
+ echo "${x%/*}/stacktrace.log"
fi
done
's_err_syswatch_'
'Thread [0-9]* (Thread'
'AliFatal'
- 'core dumped'
'\.C.*error:.*\.h: No such file'
'segmentation'
+ 'Segmentation fault'
'Interpreter error recovered'
': command not found'
': comando non trovato'
+ 'core dumped'
)
warningConditions=(
local logStatus=0
local errorSummary=""
local warningSummary=""
-
- for ((i=0; i<${#errorConditions[@]};i++)); do
- local tmp=$(grep -m1 -e "${errorConditions[${i}]}" ${log})
- [[ -n ${tmp} ]] && tmp+=" : "
- errorSummary+=${tmp}
+ local errorCondition=""
+ for errorCondition in "${errorConditions[@]}"; do
+ local tmp=$(grep -m1 -e "${errorCondition}" ${log})
+ local error=""
+ [[ -n ${tmp} ]] && error=" : ${errorCondition}"
+ errorSummary+=${error}
done
- for ((i=0; i<${#warningConditions[@]};i++)); do
- local tmp=$(grep -m1 -e "${warningConditions[${i}]}" ${log})
- [[ -n ${tmp} ]] && tmp+=" : "
- warningSummary+=${tmp}
+ local warningCondition=""
+ for warningCondition in "${warningConditions[@]}"; do
+ local tmp=$(grep -m1 -e "${warningCondition}" ${log})
+ local warning=""
+ [[ -n ${tmp} ]] && warning=" : ${warningCondition}"
+ warningSummary+=${warning}
done
if [[ -n ${errorSummary} ]]; then
echo 'benchmark.sh stackTraceTree `cat file.list`'
return 0
fi
+ #cat "${@}" | gawk '
gawk '
BEGIN {
- print "frame/I:method/C:line/C:cpass/I:aliroot/I:file/C";
+ print "frame/I:method/C:line/C:cpass/I:aliroot/I:file/C";
RS="#[0-9]*";
aliroot=0;
read=1;
gsub("#","",RT);
if ($NF!="" && RT!="" && $3!="") print RT" "$3" "$NF" "0" "aliroot" "FILENAME
}
- ' "$@" 2>/dev/null
+ ' "${@}" 2>/dev/null
+}
+
+plotStackTraceTree()
+{
+ #plot the stacktrace tree,
+ #first arg is the text file in the root tree format
+ #second arg is optional: a plot is written to file instead of screen
+ #third arg is optional: selection for plotting, default skip G_ stuff
+ local tree=$1
+ local plot=${2:-"crashes.png"}
+ local selection=${3:-'!strstr(method,\"G__\")'}
+ [[ ! -f ${tree} ]] && echo "plotStackTraceTree: no input file given" && return 1
+ aliroot -b <<EOF
+TTree* t=AliSysInfo::MakeTree("${tree}");
+TCanvas* canvas = new TCanvas("QA crashes","QA crashes",1);
+t->Draw("method","${selection}","");
+canvas->SaveAs("${plot}");
+.q
+EOF
+ return 0
}
encSpaces()
echo "${1//±@@±/ }"
}
+get_realpath()
+{
+ if [[ $# -lt 1 ]]; then
+ echo "print the full path of a file or directory, like \"readlink -f\" on linux"
+ echo "Usage:"
+ echo " get_realpath <someFileOrDir>"
+ return 0
+ fi
+ if [[ -f "$1" ]]
+ then
+ # file *must* exist
+ if cd "$(echo "${1%/*}")" &>/dev/null
+ then
+ # file *may* not be local
+ # exception is ./file.ext
+ # try 'cd .; cd -;' *works!*
+ local tmppwd="$PWD"
+ cd - &>/dev/null
+ else
+ # file *must* be local
+ local tmppwd="$PWD"
+ fi
+ elif [[ -d "$1" ]]; then
+ if cd "$1" &>/dev/null; then
+ local tmppwd="$PWD"
+ cd - &>/dev/null
+ echo "$tmppwd"
+ return 0
+ else
+ return 1
+ fi
+ else
+ # file *cannot* exist
+ return 1 # failure
+ fi
+ # reassemble realpath
+ echo "$tmppwd"/"${1##*/}"
+ return 0 # success
+}
+
+printLogStatistics()
+{
+ #this function processes the summary logs and prints some stats
+ #relies on the summary log format produced by summarizeLogs()
+ # - how many checked logs in total
+ # - number of each type of problem
+ # example usage:
+ # printLogStatistics */*.log
+ [[ ! -f $1 ]] && return 1
+ echo "log statistics from: ${1%/*}"
+ #cat "${@}" | awk '
+ awk '
+ BEGIN {nOK=0; nCores=0; nStackTraces=0;}
+ /\/core/ {nCores++}
+ /\/stacktrace.log/ {nStackTraces++}
+ /OK/ {nOK++; nLogs++;}
+ /BAD/ {
+ nLogs++
+ err=""
+ write=0
+ for (i=3; i<=NF; i++)
+ {
+ if ($i ~ /^\:$/)
+ write=1
+ else
+ write=0
+
+ if (write==0)
+ {
+ if (err=="") err=$i
+ else err=(err FS $i)
+ }
+
+ if (err != "" && (write==1 || i==NF))
+ {
+ sumBAD[err]++
+ err=""
+ }
+ }
+ }
+ END {
+ print ("number of succesful jobs: " nOK" out of "nLogs )
+ for (key in sumBAD)
+ {
+ print key": "sumBAD[key]
+ }
+ if (nCores>0) print "core files: "nCores", stack traces: "nStackTraces
+ }
+ ' "${@}"
+}
+
+createUniquePID()
+{
+ #create a unique ID for jobs running in parallel
+ #consists of the ip address of the default network interface, PID,
+ #if an argument is given, append it (e.g. a production ID)
+ #the fields are space separated with a tag for easy parsing
+ #spaces in the productionID will be encoded using encSpaces()
+ local productionID=""
+ [[ -n "${1}" ]] && productionID=$(encSpaces "${1}")
+ local defaultIP=$(/sbin/route | awk '$1=="default" {print $8}' | xargs /sbin/ifconfig | awk '/inet / {print $2}' | sed 's/.*\([0-9]?\.[0-9]?\.[0-9]?\.[0-9]?\)/$1/')
+ local id="ip:${defaultIP} pid:${BASHPID}"
+ [[ -n "${productionID}" ]] && id+=" prod:${productionID}"
+ echo "${id}"
+}
+
+copyFileToLocal()
+(
+ #copies a single file to a local destination: the file may either come from
+ #a local filesystem or from a remote location (whose protocol must be
+ #supported)
+ #copy is "robust" and it is repeated some times in case of failure before
+ #giving up (1 is returned in that case)
+ #origin: Dario Berzano, dario.berzano@cern.ch
+ src="$1"
+ dst="$2"
+ ok=0
+ [[ -z "${maxCopyTries}" ]] && maxCopyTries=10
+
+ proto="${src%%://*}"
+
+ echo "copy file to local dest started: $src -> $dst"
+
+ for (( i=1 ; i<=maxCopyTries ; i++ )) ; do
+
+ echo "...attempt $i of $maxCopyTries"
+ rm -f "$dst"
+
+ 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 2
+ ;;
+ esac
+ fi
+
+ if [ $? == 0 ] ; then
+ ok=1
+ break
+ fi
+
+ done
+
+ if [[ "$ok" == 1 ]] ; then
+ echo "copy file to local dest OK after $i attempt(s): $src -> $dst"
+ return 0
+ fi
+
+ echo "copy file to local dest FAILED after $maxCopyTries attempt(s): $src -> $dst"
+ return 1
+)
+
+paranoidCp()
+(
+ #recursively copy files and directories
+ #if target is a directory - it must exist!
+ #to avoid using find and the like as they kill
+ #the performance on some cluster file systems
+ #does not copy links to avoid problems
+ sourceFiles=("${@}")
+ destination="${sourceFiles[@]:(-1)}" #last element
+ unset sourceFiles[${#sourceFiles[@]}-1] #remove last element (dst)
+ #[[ ! -f "${destination}" ]]
+ for src in "${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
+ #returns 1 on failure, 0 on success
+ src=$(get_realpath "${1}")
+ dst=$(get_realpath "${2}")
+ [[ -d "${dst}" ]] && dst="${dst}/${src##*/}"
+ #some sanity check
+ [[ -z "${src}" ]] && echo "$1 does not exist" && return 1
+ [[ -z "${dst}" ]] && echo "$2 does not exist" && return 1
+ #check if we are not trying to copy to the same file
+ [[ "${src}" == "${dst}" ]] && echo "$dst==$src, not copying" && return 0
+ ok=0
+ [[ -z "${maxCopyTries}" ]] && maxCopyTries=10
+
+ echo "paranoid copy started: $src -> $dst"
+ for (( i=1 ; i<=maxCopyTries ; i++ )) ; do
+
+ echo "...attempt $i of $maxCopyTries"
+ rm -f "$dst"
+ cp "$src" "$dst"
+
+ cmp -s "$src" "$dst"
+ if [ $? == 0 ] ; then
+ ok=1
+ break
+ fi
+
+ done
+
+ if [[ "$ok" == 1 ]] ; then
+ echo "paranoid copy OK after $i attempt(s): $src -> $dst"
+ return 0
+ fi
+
+ echo "paranoid copy FAILED after $maxCopyTries attempt(s): $src -> $dst"
+ return 1
+)
+
+generPWD(){
+ #
+ # generate semirandom pwd using 2 keys
+ # Example usage:
+ # generPWD myserviceaccount10 key11
+ key0=$1
+ key1=$2
+ heslo0=`md5sum <<< "$key0 $key1" | cut -c 1-16`
+ heslo=`echo $heslo0 | cut -c 1-8| awk '{print toupper($0)}'`
+ heslo=$heslo`echo $heslo0 | cut -c 8-15| awk '{print tolower($0)}'`%
+ echo $heslo;
+}
+
+#this makes debugging easier:
+#executes the command given as an argument in this environment
+#use case:
+# bashdb utilities.sh summarizeLogs * */*
+[[ $# != 0 ]] && eval "$@"
git://git.uio.no / u / mrichter / AliRoot.git / blobdiff