RelVal: opt parsing fix and syntax update

[u/mrichter/AliRoot.git] / PWGPP / benchmark / benchmark.sh

diff --git a/PWGPP/benchmark/benchmark.sh b/PWGPP/benchmark/benchmark.sh
index 8a374093c9e0c6125ca2352915d9e0f9c8e86af9..52017b3a2ca96471b0d57604e9154ecc789e3778 100755 (executable)
--- a/PWGPP/benchmark/benchmark.sh
+++ b/PWGPP/benchmark/benchmark.sh
@@ -155,7 +155,11 @@ goCPass0()
 
   #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
@@ -191,7 +195,7 @@ goCPass0()
   fi
   ######
   
-  if [[ ! -f ${inputList} && -z ${pretend} ]]; then
+  if [[ "${inputList}" == "${inputList%%://*}" && ! -f "${inputList}" && -z ${pretend} ]]; then
     touch ${doneFileTmp}
     echo "input file ${inputList} not found, exiting..." >> ${doneFileTmp}
     cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
@@ -256,7 +260,7 @@ goCPass0()
   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 ${pretendDelay}
     touch AliESDs.root
@@ -265,8 +269,8 @@ goCPass0()
     touch rec.log
     touch calib.log
   else
-    echo ./runCPass0.sh "${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
@@ -347,7 +351,7 @@ goCPass1()
   #Packages= ;OutputDir= ;LPMPass= ;TriggerAlias= ;LPMRunNumber= ;LPMProductionType= ;LPMInteractionType= ;LPMProductionTag= ;LPMAnchorRun= ;LPMAnchorProduction= ;LPMAnchorYear= 
   export PRODUCTION_METADATA="OutputDir=cpass1"
 
-  if [[ ! -f ${inputList} && -z ${pretend} ]]; then
+  if [[ "${inputList}" == "${inputList%%://*}" && ! -f "${inputList}" && -z ${pretend} ]]; then
     touch ${doneFileTmp}
     echo "input file ${inputList} not found, exiting..." >> ${doneFileTmp}
     cp "$doneFileTmp" "$doneFile" || rm -f "$doneFileTmp" "$doneFile"
@@ -399,7 +403,11 @@ goCPass1()
   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}
@@ -503,7 +511,7 @@ goCPass1()
 
   #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 ${pretendDelay}
     touch AliESDs_Barrel.root
@@ -521,7 +529,8 @@ goCPass1()
     touch qa.log
     touch filtering.log FilterEvents_Trees.root
   else
-    ./runCPass1.sh "${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
@@ -707,7 +716,7 @@ goMergeCPass0()
     /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 ${pretendDelay}
     touch CalibObjects.root
@@ -719,7 +728,7 @@ goMergeCPass0()
     echo "some calibration" >> ./OCDB/TPC/Calib/TimeGain/someCalibObject_0-999999_cpass0.root
     echo "some calibration" >> ./OCDB/TPC/Calib/TimeDrift/otherCalibObject_0-999999_cpass0.root
   else
-    ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" ${ocdbStorage} >> "mergeMakeOCDB.log"
+    ./${mergingScript} ${calibrationFilesToMerge} ${runNumber} "local://./OCDB" defaultOCDB=${ocdbStorage} fileAccessMethod=nocopy >> "mergeMakeOCDB.log"
 
     #produce the calib trees for expert QA (dcsTime.root)
     goMakeLocalOCDBaccessConfig ./OCDB
@@ -895,8 +904,8 @@ goMergeCPass1()
     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
@@ -910,7 +919,7 @@ goMergeCPass1()
     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 ${AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF} ]] && export AliAnalysisTaskFilteredTree_fLowPtTrackDownscaligF
@@ -1025,9 +1034,9 @@ goSubmitMakeflow()
   #if which greadlink; then self=$(greadlink -f "${0}"); fi
   
   #for reference copy the setup to the output dir
-  cp ${self} ${commonOutputPath}
-  cp ${configFile} ${commonOutputPath}
-  cp ${inputFileList} ${commonOutputPath}
+  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
@@ -2556,6 +2565,7 @@ parseConfig()
   logToFinalDestination=1
   ALIROOT_FORCE_COREDUMP=1
   pretendDelay=0
+  copyInputData=0
 
   #first, source the config file
   if [ -f ${configFile} ]; then
@@ -2612,6 +2622,31 @@ aliroot()
   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