Merge pull request #20 from amereghe/master

preparing 'dev' release of 4th May 2018
SixTrack · May 4, 2018 · 5a17a3b · 5a17a3b
2 parents ca77111 + b73486f
commit 5a17a3b
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diff --git a/boinc_software/cronjobs/acrontab_jobs_sixtadm.txt b/boinc_software/cronjobs/acrontab_jobs_sixtadm.txt
@@ -20,10 +20,14 @@
 20 3 * * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinc ; /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.sh >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
 40 3 * * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinctest ; /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.sh >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
 #
-# list studies in spooldirs that could be deleted and notify users (based on dir itself):
+# list studies in spooldirs that could be deleted and notify users (based on <workspace>_<study> dir itself):
 0 4 1 * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinc ; /afs/cern.ch/user/s/sixtadm/boinc_soft/listDeleteStudies.sh >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
 0 5 1 * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinctest ; /afs/cern.ch/user/s/sixtadm/boinc_soft/listDeleteStudies.sh >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
 #
 # list studies in spooldirs that could be deleted and notify users (based on <workspace>_<study>/work dir):
-0 4 15 * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinc ; /afs/cern.ch/user/s/sixtadm/boinc_soft/listDeleteStudies.sh >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
-0 5 15 * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinctest ; /afs/cern.ch/user/s/sixtadm/boinc_soft/listDeleteStudies.sh >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
+0 4 11 * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinc ; /afs/cern.ch/user/s/sixtadm/boinc_soft/listDeleteStudies.sh work >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
+0 5 11 * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinctest ; /afs/cern.ch/user/s/sixtadm/boinc_soft/listDeleteStudies.sh work >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
+#
+# list studies in spooldirs that could be deleted and notify users (based on <workspace>_<study>/results dir):
+0 4 21 * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinc ; /afs/cern.ch/user/s/sixtadm/boinc_soft/listDeleteStudies.sh results >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
+0 5 21 * * lxplus.cern.ch cd /afs/cern.ch/work/b/boinc/boinctest ; /afs/cern.ch/user/s/sixtadm/boinc_soft/listDeleteStudies.sh results >> /afs/cern.ch/user/s/sixtadm/boinc_soft/deleteStudies.log 2>&1
diff --git a/boinc_software/cronjobs/listDeleteStudies.sh b/boinc_software/cronjobs/listDeleteStudies.sh
@@ -5,7 +5,7 @@
 # to be run in:
 #     /afs/cern.ch/work/b/boinc/boinc
 oldN=30 # days
-threshOccupancy=0.5 # [GB]
+threshOccupancy=1.0 # [GB]
 BOINCspoolDir=$PWD
 SCRIPTDIR=`dirname $0`
 SCRIPTDIR="`cd ${SCRIPTDIR} ; pwd`"
@@ -28,11 +28,8 @@ function treatSingleDir(){
 }
 
 trap "echo \" ...ending at \`date\` .\" " exit
+echo ""
 echo " starting `basename $0` at `date` ..."
-lUseWork=true
-if [ $# == 1 ] ; then
-    lUseWork=false
-fi
 
 # prepare delete dir
 [ -d delete ] || mkdir delete
@@ -46,12 +43,20 @@ echo " checking BOINC spooldir ${BOINCspoolDir} ..."
 #    ask confirmation to user
 now=`date +"%F_%H-%M-%S"`
 # find old directories (based on <workspace>_<studyName>/work/)
-if ${lUseWork} ; then
-    echo " find old directories based on <workspace>_<studyName>/work/ ..."
-    allStudies=`find . -maxdepth 2 -type d -name work -ctime +${oldN}`
-    for currCase in ${allStudies} ; do
-	treatSingleDir ${currCase%/work}
-    done
+if [ -n "$1" ] ; then
+    case "$1" in
+	work | results )
+	    echo " find old directories based on <workspace>_<studyName>/$1/ ..."
+	    allStudies=`find . -maxdepth 2 -type d -name $1 -ctime +${oldN}`
+	    for currCase in ${allStudies} ; do
+		treatSingleDir ${currCase%/$1}
+	    done
+	    ;;
+	* )
+	    echo " wrong input: $1 [work|results]"
+	    exit 1
+	    ;;
+    esac
 else
     echo " find old directories based on <workspace>_<studyName> only ..."
     allStudies=`find . -maxdepth 1 -type d -ctime +${oldN} | grep -v -e upload -e delete`

diff --git a/boinc_software/maintain_common_space/structureMe.sh b/boinc_software/maintain_common_space/structureMe.sh
@@ -82,11 +82,17 @@ EOF
     fi
     if ${lScripts} ; then
 	# make fortran exes for checking fort.10
-	cd ${__Dir}
-	cd utilities/fortran
+	cd ${__Dir}/utilities/fortran
 	make
 	ls -ltrh
 	cd ${__origDir}
+	# make documentation
+        if [ -d ${__Dir}/utilities/doc ] ; then
+	    cd ${__Dir}/utilities/doc
+	    make
+	    ls -ltrh
+        fi
+	cd ${__origDir}
 	# echo commits/logs
 	echo ""
 	echo " --> present branch:"
@@ -119,6 +125,10 @@ function checkDir(){
     cd ${__Dir}/utilities/fortran
     ls -ltrh
     cd ${__origDir}
+    # documentation
+    cd ${__Dir}/utilities/doc
+    ls -ltrh
+    cd ${__origDir}
     # checkout of SixDB
     cd ${__Dir}/utilities/externals/SixDeskDB/
     git log --max-count=1

diff --git a/utilities/templates/input/fort.3.local → sixjobs/fort.3.local b/utilities/templates/input/fort.3.local → sixjobs/fort.3.local
diff --git a/sixjobs/scan_definitions b/sixjobs/scan_definitions
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+############################## SCAN OVER A CARTESIAN GRID ######################
+
+# specify the variable names to be used in naming the studies, e.g.:
+# scan_variables="QP IOCT"
+scan_variables="QP IOCT"
+
+# specify the placeholders in the mask file, e.g.:
+# scan_placeholders="%QPV %OCV"
+scan_placeholders="%QPV %OCV"
+
+# specify the prefix of the study name
+# e.g. if the base mask file is called hl13B1.mask, we use:
+# scan_prefix="hl10BaseB1"
+scan_prefix="hl10BaseB1"
+
+# specify the values to be taken by the different variables
+# if we want to use 14 for QP and values between 0 and 40 in steps of 40 for IOCT:
+# scan_vals_QP="3"
+# scan_vals_IOCT=$(seq -500 200 500)
+scan_vals_QP="3"
+scan_vals_IOCT=$(seq -500 200 500)
+
+
+############################## SCAN OVER SPECIFIC MASKS  #######################
+
+# THIS OPTION REQUIRES ALL THE MASK FILES TO BE EXISTING
+
+# (de)activate the scan over specific masks
+scan_masks=false
+scan_studies="
+ats2017_QP_0_IOCT_12
+ats2017_QP_0_IOCT_16
+"
diff --git a/utilities/templates/input/sixdeskenv → sixjobs/sixdeskenv b/utilities/templates/input/sixdeskenv → sixjobs/sixdeskenv
diff --git a/utilities/templates/input/sysenv → sixjobs/sysenv b/utilities/templates/input/sysenv → sixjobs/sysenv
diff --git a/utilities/bash/dot_profile b/utilities/bash/dot_profile
@@ -625,17 +625,17 @@ sixdeskamps()
 sixdeskAllFloats(){
     # A.Mereghetti, 2017-04-08
     # new function, to generate an array of floating point values
-    local __precision=1.0E-15
     local __xMin=$1
     local __xMax=$2
     local __xDelta=$3
+    local __lSkipExtremes=$4
     # - preliminary checks - to be moved to check_env.sh
     if [ -z "${__xMax}" ] || [ -z "${__xDelta}" ] ; then
 	__xMax=${__xMin}
 	__xDelta=${__xMin}
     fi
     # - get all values
-    python ${SCRIPTDIR}/python/generate_floats.py ${__xMin} ${__xMax} ${__xDelta} ${__precision}
+    python ${SCRIPTDIR}/python/generate_floats.py ${__xMin} ${__xMax} ${__xDelta} ${__lSkipExtremes}
 }
 sixdeskFixDotFloat(){
     # A.Mereghetti, 2017-04-08
@@ -661,10 +661,11 @@ sixdeskAllTunes(){
     # - tunesYY: returned array of ver tune values
     # - inttunesXX: returned array of integer part of hor tunes
     # - inttunesYY: returned array of integer part of ver tunes
+    local __lForceIntegers=False
     # hor:
     tunesXX=""
     inttunesXX=""
-    local __tunesXX=$(sixdeskAllFloats $tunex $tunex1 $deltax)
+    local __tunesXX=$(sixdeskAllFloats $tunex $tunex1 $deltax )
     for tmptn in ${__tunesXX} ; do
 	tunesXX="${tunesXX} $(sixdeskFixDotFloat ${tmptn})"
 	inttunesXX="${inttunesXX} $(sixdeskinttune ${tmptn})"
@@ -674,7 +675,7 @@ sixdeskAllTunes(){
     # ver:
     tunesYY=""
     inttunesYY=""
-    local __tunesYY=$(sixdeskAllFloats $tuney $tuney1 $deltay)
+    local __tunesYY=$(sixdeskAllFloats $tuney $tuney1 $deltay )
     for tmptn in ${__tunesYY} ; do
 	tunesYY="${tunesYY} $(sixdeskFixDotFloat ${tmptn})"
 	inttunesYY="${inttunesYY} $(sixdeskinttune ${tmptn})"
@@ -691,9 +692,10 @@ sixdeskAllAmplitudes(){
     ampstart=""
     ampfinish=""
     local __iLast=0
+    local __lForceIntegers=False
 
     # get all amplitude points
-    local __allAmplitudes=$(sixdeskAllFloats $ns1l $ns2l $nsincl)
+    local __allAmplitudes=$(sixdeskAllFloats $ns1l $ns2l $nsincl )
     __allAmplitudes=( ${__allAmplitudes} )
 
     # get all amplitude intervals
@@ -728,7 +730,6 @@ sixdeskAllAngles(){
     local __lbackcomp=$7
     local __lReduceAngsWithAmplitude=$8
     local __totAngle=$9
-    local __factor=${10}
 
     # generated arrays:
     KKs=""
@@ -740,47 +741,55 @@ sixdeskAllAngles(){
     if ${__lReduceAngsWithAmplitude}; then
         for (( iAmple=0; iAmple<${#fAmpEnds[@]}; iAmple++ )) ; do
             if (( $(echo "${reduce_angs_with_amplitude} ${fAmpEnds[${iAmple}]}" | awk '{print ($1 < $2)}') )); then
+                # varying number of angles
                 local __angles_nb=$(echo ${fAmpEnds[${iAmple}]} ${ampfinish} ${__kmax} | awk '{printf ("%.f", ($1/$2*$3))}')
             else
+                # constant number of angles
                 local __angles_nb=$(echo ${reduce_angs_with_amplitude} ${ampfinish} ${__kmax} | awk '{printf ("%.f", ($1/$2*$3))}')
             fi
 
             if [ ${__angles_nb} -eq 0 ];then
                 __angles_nb=1
             fi
-
-            for (( kk=1; kk<=${__angles_nb}; kk++ )) ; do
-	        KKs="${KKs} ${kk}"
-                local __tmpAngle=`echo ${totAngle} ${kk} ${__angles_nb} | awk '{print ($1*$2/($3+1))}'`
-	        Angles="${Angles} ${__tmpAngle}"  
-	        if ${__lbackcomp} ; then
+            if ${__lbackcomp} ; then
+                for (( kk=1; kk<=${__angles_nb}; kk++ )) ; do
+	            KKs="${KKs} ${kk}"
+                    local __tmpAngle=`echo ${totAngle} ${kk} ${__angles_nb} | awk '{print ($1*$2/($3+1))}'`
+	            Angles="${Angles} ${__tmpAngle}"  
 	            local __kang=`echo ${kk} ${__angles_nb} | awk '{print ($1/($2+1))}'`
-	        else
-	            local __kang=`echo ${kk} ${__angles_nb} | awk '{printf ("%.16E",$1/($2+1))}'`
-	        fi
-	        kAngs="${kAngs} ${__kang}"
-            done
+	            kAngs="${kAngs} ${__kang}"
+                done
+            else
+                KKs="${KKs} $(seq 1 ${__angles_nb})"
+                local __angleStep=`echo ${__totAngle} ${__angles_nb} | awk '{print ($1/($2+1))}'`
+                Angles="${Angles} $(sixdeskAllFloats 0 ${__totAngle} ${__angleStep} True)" 
+                local __kAngleStep=`echo ${__angles_nb} | awk '{printf ("%.18f",1.0/($1+1))}'`
+                kAngs="${kAngs} $(sixdeskAllFloats 0.0 1.0 ${__kAngleStep} True)"
+            fi
             let nTotAngles+=${__angles_nb}
             KKs_ampl+=( ${nTotAngles} )
         done
     else
         if ${__lbackcomp} ; then
             local __angleStep=`echo ${__totAngle} ${__kmax} | awk '{print ($1/($2+1))}'`
+            for (( kk=${__kmin}; kk<=${__kend}; kk+=${__kstep} )) ; do
+	        KKs="${KKs} ${kk}"
+	        local __tmpAngle=`echo ${kk} ${__angleStep} | awk '{print ($1*$2)}'`
+	        Angles="${Angles} ${__tmpAngle}"
+	        if ${__lbackcomp} ; then
+	            local __kang=`echo ${kk} ${__kmax} | awk '{print ($1/($2+1))}'`
+	        else
+	            local __kang=`echo ${kk} ${__kmax} | awk '{printf ("%.16E",$1/($2+1))}'`
+	        fi
+	        kAngs="${kAngs} ${__kang}"
+            done
         else
-            local __angleStep=`echo ${__totAngle} ${__kmax} | awk '{printf ("%.16E",$1/($2+1))}'`
+            KKs="${KKs} $(seq 1 ${__kmax})"
+            local __angleStep=`echo ${__totAngle} ${__kmax} | awk '{print ($1/($2+1))}'`
+            Angles="${Angles} $(sixdeskAllFloats 0 ${__totAngle} ${__angleStep} True)" 
+            local __kAngleStep=`echo ${__kmax} | awk '{printf ("%.18f",1.0/($1+1))}'`
+            kAngs="${kAngs} $(sixdeskAllFloats 0.0 1.0 ${__kAngleStep} True)"
         fi
-
-        for (( kk=${__kmin}; kk<=${__kend}; kk+=${__kstep} )) ; do
-	    KKs="${KKs} ${kk}"
-	    local __tmpAngle=`echo ${kk} ${__angleStep} | awk '{print ($1*$2)}'`
-	    Angles="${Angles} ${__tmpAngle}"
-	    if ${__lbackcomp} ; then
-	        local __kang=`echo ${kk} ${__kmax} | awk '{print ($1/($2+1))}'`
-	    else
-	        local __kang=`echo ${kk} ${__kmax} | awk '{printf ("%.16E",$1/($2+1))}'`
-	    fi
-	  kAngs="${kAngs} ${__kang}"
-        done
         KKs_ampl=( ${KKs_ampl} ${__kend} )
     fi
 
@@ -803,35 +812,64 @@ sixdeskDefinePythonPath(){
 	export PATH=${1}:${PATH}
 	sixdeskmess 2 "Setting python to ${1} in PATH env var"
     fi
-    sixdeskmess -1 "--> python set to: `which python` - version: `python --version`"
+    sixdeskmess -1 "Python set to: `which python` - version: `python --version 2>&1`"
+}
+sixdeskGetCurretPaths(){
+    tmpDir=`readlink -f $PWD`
+    tmpDir=`dirname ${tmpDir}`
+    tmpWorkspace=`basename ${tmpDir}`
+    if [[ "${tmpDir}" == *"scratch"* ]] ; then
+        # scratchdir IS in the path
+        tmpDir=`dirname ${tmpDir}`
+        tmpScratchName=`basename ${tmpDir}`
+        tmpDir=`dirname ${tmpDir}`
+        tmpBaseDir=${tmpDir}
+        tmpScratchDir=\$basedir/${tmpScratchName}
+        tmpTrackDir=\$scratchdir/\$workspace
+        tmpSixtrackInput=\$scratchdir/sixtrack_input/\$workspace/\$LHCDescrip
+        tmpSixdeskWork=\$scratchdir/work/\$workspace/\$LHCDescrip
+        tmpCronLogs=\$scratchdir/cronlogs/\$workspace
+        tmpSixdeskLogs=\$scratchdir/sixdesklogs/\$workspace
+    else
+        # scratchdir is NOT in the path
+        tmpDir=`dirname ${tmpDir}`
+        tmpBaseDir=${tmpDir}
+        tmpScratchDir=\$basedir/\$workspace
+        tmpTrackDir=\$basedir/\$workspace
+        tmpSixtrackInput=\$scratchdir/sixtrack_input/\$LHCDescrip
+        tmpSixdeskWork=\$scratchdir/work/\$LHCDescrip
+        tmpCronLogs=\$scratchdir/cronlogs
+        tmpSixdeskLogs=\$scratchdir/sixdesklogs
+    fi
 }
 sixdeskDefineUserTree(){
     # define the tree in the userspace
-
-    # input variables are the starting points:
-    # $1: root dir (ie $basedir in sixdeskenv)
-    # $2: scratch dir (ie $scratchdir in sixdeskenv)
-    # $3: workspace name (ie $workspace in sixdeskenv)
 
+    # get current paths
+    sixdeskGetCurretPaths
+
     # basic paths (back-compatibility)
-    [ -n "${basedir}" ] || export basedir=$1               # eg /afs/cern.ch/user/$initial/$LOGNAME
-    [ -n "${scratchdir}" ] || export scratchdir=$2            # eg $basedir/scratch0
-    [ -n "${trackdir}" ] || export trackdir=$scratchdir/$3  # eg $scratchdir/w2
-    [ -n "${sixdeskhome}" ] || export sixdeskhome=$basedir/$3/sixjobs # eg $trackdir/sixjobs
-    [ -n "${sixdeskhomeStudies}" ] || export sixdeskhomeStudies=$sixdeskhome/studies
-
-    # 
-    [ -n "${sixtrack_input}" ] || export sixtrack_input=$scratchdir/sixtrack_input/$workspace/$LHCDescrip
-    [ -n "${sixdesklogs}" ] || export sixdesklogs=$scratchdir/sixdesklogs/$workspace
-    [ -n "${sixdesklogdir}" ] || export sixdesklogdir=$sixdesklogs/$LHCDescrip
-    [ -n "${cronlogs}" ] || export cronlogs=$scratchdir/cronlogs/$workspace
-    [ -n "${cronlogdir}" ] || export cronlogdir=$cronlogs/$LHCDescrip
+    [ -n "${workspace}" ] || export workspace=${tmpWorkspace}
+    [ -n "${basedir}" ] || export basedir=${tmpBaseDir}
+    [ -n "${scratchdir}" ] || export scratchdir=${tmpScratchDir}
+    [ -n "${trackdir}" ] || export trackdir=${tmpTrackDir}
+    [ -n "${sixtrack_input}" ] || export sixtrack_input=${tmpSixtrackInput}
+    [ -n "${sixdeskwork}" ] || export sixdeskwork=${tmpSixdeskWork}
+
+    # dependent paths
+    [ -n "${sixdeskhome}" ] || export sixdeskhome=${basedir}/${workspace}/sixjobs
+    [ -n "${sixdeskhomeStudies}" ] || export sixdeskhomeStudies=${sixdeskhome}/studies
+    [ -n "${sixdeskstudy}" ] || export sixdeskstudy=$sixdeskhomeStudies/$LHCDescrip
     [ -n "${sixdesktrack}" ] || export sixdesktrack=$trackdir/track
     [ -n "${sixdesktrackStudy}" ] || export sixdesktrackStudy=$sixdesktrack/$LHCDescrip
-    [ -n "${sixdeskwork}" ] || export sixdeskwork=$scratchdir/work/$workspace/$LHCDescrip
+
+    # logs/jobs paths
+    [ -n "${sixdesklogs}" ] || export sixdesklogs=${tmpSixdeskLogs}
+    [ -n "${sixdesklogdir}" ] || export sixdesklogdir=$sixdesklogs/$LHCDescrip
+    [ -n "${cronlogs}" ] || export cronlogs=${tmpCronLogs}
+    [ -n "${cronlogdir}" ] || export cronlogdir=$cronlogs/$LHCDescrip
     [ -n "${sixdeskjobs}" ] || export sixdeskjobs=$sixdeskwork/$sixdeskplatform"jobs"
     [ -n "${sixdeskjobs_logs}" ] || export sixdeskjobs_logs=$sixdeskjobs/jobs_logs
-    [ -n "${sixdeskstudy}" ] || export sixdeskstudy=$sixdeskhomeStudies/$LHCDescrip
 }
 sixDeskDefineMADXTree(){
     local __SCRIPTDIR=$1
@@ -1544,3 +1582,23 @@ function sixdeskCompareVersions(){
     # 0: true ; 1: false
     echo $1 $2 | awk '{print ($1>=$2)}'
 }
+function sixdeskConfirmExit(){
+    local __iExit=-1
+    while [ ${__iExit} -lt 0 ] ; do
+        sixdeskmess -1 "Continue? [y/n]"
+        read answer
+        case ${answer} in
+	    [yY] | [yY][Ee][Ss] )
+	        sixdeskmess -1 "Continuing..."
+                __iExit=0
+                ;;
+	    [nN] | [n|N][O|o] )
+                sixdeskmess -1  "Interrupted"
+                __iExit=1
+                ;;
+	    *) sixdeskmess -1 "Invalid input!"
+	       ;;
+        esac
+    done
+    return ${__iExit}
+}