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Fort13 #19

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484b519
fort13 added
Feb 27, 2018
5a4b8e4
fort.13
Feb 27, 2018
e4d3b9c
fort.13 for submission
Mar 3, 2018
e0fe1bb
split modified
Apr 25, 2018
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20 changes: 20 additions & 0 deletions utilities/bash/dot_profile
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Original file line number Diff line number Diff line change
Expand Up @@ -685,6 +685,26 @@ sixdeskAllTunes(){
tunesYY=( ${tunesYY} )
inttunesYY=( ${inttunesYY} )
}
sixdeskAllAmplitudes_fort13(){
## This function splits the fort.13 file according to the number of pairs set in sixdeskenv. A new directory fort13_jobs in the work directory is created which contains all the fort.13 jobs. The amplitude steps are named after the number of the job.
pairs_per_job=$((sixdeskpairs*15)) ## each pair correspons to 15 lines
if [ -d "${sixdeskjobs_logs}/fort.13_jobs" ]; then
rm -rf ${sixdeskjobs_logs}/fort.13_jobs/*
else
mkdir ${sixdeskjobs_logs}/fort.13_jobs
fi
split -a 6 -d -l $pairs_per_job fort.13 ${sixdeskjobs_logs}/fort.13_jobs/fort.13.
fort13_jobs=( $(find ${sixdeskjobs_logs}/fort.13_jobs/ -type f -name 'fort.13.*') )
nb_fort13_jobs=${#fort13_jobs[@]}
echo Fort.13 will be split in $nb_fort13_jobs jobs
allAmplitudeSteps=( $(seq 1 1 $nb_fort13_jobs) )
fAmpStarts=("${allAmplitudeSteps[@]}")
fAmpEnds=("${allAmplitudeSteps[@]}")
ampstart=${fAmpStarts[0]}
let __iLast=${#fAmpEnds[@]}-1
ampfinish=${fAmpEnds[${__iLast}]}
}

sixdeskAllAmplitudes(){
# A.Mereghetti, 2017-04-08
# new function, to generate all amplitude steps
Expand Down
10 changes: 8 additions & 2 deletions utilities/bash/mad6t.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -150,9 +150,13 @@ function submit(){
# Loop over seeds
mad6tjob=$lsfFilesPath/mad6t1.sh
for (( iMad=$istamad ; iMad<=$iendmad ; iMad++ )) ; do

if [ "${lflag_fort13}" = true ] ; then
files="2 8 13 16 34" ## fort.13 is also included in sixtrack_input
else
files="2 8 16 34"
fi
# clean away any existing results for this seed
for f in 2 8 16 34 ; do
for f in files ; do
rm -f $sixtrack_input/fort.$f"_"$iMad.gz
done

Expand All @@ -168,6 +172,8 @@ function submit(){
-e 's?%FORT_34%?'$fort_34'?g' \
-e 's?%MADX_PATH%?'$MADX_PATH'?g' \
-e 's?%MADX%?'$MADX'?g' \
-e 's?%lflag_fort13%?'$lflag_fort13'?g' \
-e 's?%sixdeskstudy%?'$sixdeskstudy'?g' \
-e 's?%SIXTRACK_INPUT%?'$sixtrack_input'?g' $mad6tjob > mad6t_"$iMad".sh
chmod 755 mad6t_"$iMad".sh

Expand Down
215 changes: 148 additions & 67 deletions utilities/bash/run_six.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -264,23 +264,43 @@ function preProcessFort3(){
local __dp1=.0
local __dp2=.0
fi
sed -e 's/%turnss/%turnsl/g' \
-e 's/%nss/'$sixdeskpairs'/g' \
-e 's/%imc/'$__imc'/g' \
-e 's/%iclo6/'$__iclo6'/g' \
-e 's/%ax0s/%ax0l/g' \
-e 's/%ax1s/%ax1l/g' \
-e 's/%writebins/%writebinl/g' \
-e 's/%ratios/%ratiol/g' \
-e 's/%dp1/'$__dp1'/g' \
-e 's/%dp2/'$__dp2'/g' \
-e 's/%e0/'$e0'/g' \
-e 's/%ition/'$__ition'/g' \
-e 's/%idfor/'$idfor'/g' \
-e 's/%ibtype/'$ibtype'/g' \
-e 's/%bunch_charge/'$bunch_charge'/g' \
-e 's?%Runnam?%Runnam '"$sixdeskTitle"'?g' \
$sixdeskjobs_logs/fort.3.mother1 > $sixdeskjobs_logs/fortl.3.mask
## if fort.13 flag is on keep %nss. There could be an unequal number of pairs in each fort.13 jobs
if $lflag_fort13; then
sed -e 's/%turnss/%turnsl/g' \
-e 's/%imc/'$__imc'/g' \
-e 's/%iclo6/'$__iclo6'/g' \
-e 's/%ax0s/%ax0l/g' \
-e 's/%ax1s/%ax1l/g' \
-e 's/%writebins/%writebinl/g' \
-e 's/%ratios/%ratiol/g' \
-e 's/%dp1/'$__dp1'/g' \
-e 's/%dp2/'$__dp2'/g' \
-e 's/%e0/'$e0'/g' \
-e 's/%ition/'$__ition'/g' \
-e 's/%idfor/'$idfor'/g' \
-e 's/%ibtype/'$ibtype'/g' \
-e 's/%bunch_charge/'$bunch_charge'/g' \
-e 's?%Runnam?%Runnam '"$sixdeskTitle"'?g' \
$sixdeskjobs_logs/fort.3.mother1 > $sixdeskjobs_logs/fortl.3.mask
else
sed -e 's/%turnss/%turnsl/g' \
-e 's/%nss/'$sixdeskpairs'/g' \
-e 's/%imc/'$__imc'/g' \
-e 's/%iclo6/'$__iclo6'/g' \
-e 's/%ax0s/%ax0l/g' \
-e 's/%ax1s/%ax1l/g' \
-e 's/%writebins/%writebinl/g' \
-e 's/%ratios/%ratiol/g' \
-e 's/%dp1/'$__dp1'/g' \
-e 's/%dp2/'$__dp2'/g' \
-e 's/%e0/'$e0'/g' \
-e 's/%ition/'$__ition'/g' \
-e 's/%idfor/'$idfor'/g' \
-e 's/%ibtype/'$ibtype'/g' \
-e 's/%bunch_charge/'$bunch_charge'/g' \
-e 's?%Runnam?%Runnam '"$sixdeskTitle"'?g' \
$sixdeskjobs_logs/fort.3.mother1 > $sixdeskjobs_logs/fortl.3.mask
fi
let __lerr+=$?
# - multipole blocks
cat $sixdeskjobs_logs/fort.3.mad >> $sixdeskjobs_logs/fortl.3.mask
Expand Down Expand Up @@ -508,7 +528,11 @@ function preProcessBoinc(){
function submitChromaJobs(){

local __destination=$1
local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'
if ${lflag_fort13}; then
local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:fort.13*:sixdesklock:chromaJob0?:lin*:betaJob'
else
local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'
fi

# --------------------------------------------------------------------------
# generate appropriate fort.3 files as: fort.3.tx + fort.3.mad + fort.3.m2
Expand Down Expand Up @@ -579,6 +603,9 @@ function submitChromaJobs(){
sixdeskmess 1 "Running the first one turn job for chromaticity"
cat fort.3.t1 fort.3.mad fort.3.m2 > fort.3
rm -f fort.10
if ${lflag_fort13}; then
cp $sixdeskhome/fort.13 .
fi
$SIXTRACKEXE > first_oneturn
if test $? -ne 0 -o ! -s fort.10 ; then
sixdeskmess -1 "The first turn Sixtrack for chromaticity FAILED!!!"
Expand All @@ -589,18 +616,24 @@ function submitChromaJobs(){
# save all interesting files from first job
rm -rf chromaJob01
mkdir chromaJob01
cp fort.2 fort.3 fort.8 fort.16 fort.10 first_oneturn chromaJob01
if ${lflag_fort13}; then
cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 first_oneturn chromaJob01
else
cp fort.2 fort.3 fort.8 fort.16 fort.10 first_oneturn chromaJob01
fi
gzip -f chromaJob01/*
mv fort.10 fort.10_first_oneturn
# clean dir
export GLOBIGNORE=${__GLOBIGNORE}
rm -f *
export GLOBIGNORE=

# - second job
sixdeskmess 1 "Running the second one turn job for chromaticity"
cat fort.3.t2 fort.3.mad fort.3.m2 > fort.3
rm -f fort.10
if ${lflag_fort13}; then
cp $sixdeskhome/fort.13 .
fi
$SIXTRACKEXE > second_oneturn
if test $? -ne 0 -o ! -s fort.10 ; then
sixdeskmess -1 "The second turn Sixtrack for chromaticity FAILED!!!"
Expand All @@ -611,7 +644,11 @@ function submitChromaJobs(){
# save all interesting files from second job
rm -rf chromaJob02
mkdir chromaJob02
cp fort.2 fort.3 fort.8 fort.16 fort.10 second_oneturn chromaJob02
if ${lflag_fort13}; then
cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 second_oneturn chromaJob02
else
cp fort.2 fort.3 fort.8 fort.16 fort.10 second_oneturn chromaJob02
fi
gzip -f chromaJob02/*
mv fort.10 fort.10_second_oneturn
# clean dir
Expand All @@ -633,8 +670,11 @@ function submitChromaJobs(){
function submitBetaJob(){

local __destination=$1
local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'

if ${lflag_fort13};then
local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:fort.13*:sixdesklock:chromaJob0?:lin*:betaJob'
else
local __GLOBIGNORE='fort.[2,8]:fort.16:fort*.3.*:fort.10*:sixdesklock:chromaJob0?:lin*:betaJob'
fi
# --------------------------------------------------------------------------
# generate appropriate fort.3 files as: fort.3.m1 + fort.3.mad + fort.3.m2
sed -e 's/%turnss/'1'/g' \
Expand Down Expand Up @@ -681,6 +721,9 @@ function submitBetaJob(){
# --------------------------------------------------------------------------
# actually run
rm -f fort.10
if ${lflag_fort13};then
cp $sixdeskhome/fort.13 .
fi
$SIXTRACKEXE > lin
if test $? -ne 0 -o ! -s fort.10 ; then
sixdeskmess -1 "The one turn Sixtrack for betavalues FAILED!!!"
Expand All @@ -691,7 +734,11 @@ function submitBetaJob(){
# save all interesting files from beta job
rm -rf betaJob
mkdir betaJob
cp fort.2 fort.3 fort.8 fort.16 fort.10 lin betaJob
if ${lflag_fort13};then
cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 lin betaJob
else
cp fort.2 fort.3 fort.8 fort.16 fort.10 fort.13 lin betaJob
fi
gzip -f betaJob/*
mv lin lin_old
cp fort.10 fort.10_old
Expand Down Expand Up @@ -759,19 +806,27 @@ function submitCreateFinalFort3Short(){
}

function submitCreateFinalFort3Long(){

local __lerr=0

# returns ratio
sixdeskRatio $kang $lbackcomp
[ -n "${ratio}" ] || let __lerr+=1
# returns ax0 and ax1
sixdeskax0 $factor $beta_x $beta_x2 $beta_y $beta_y2 $ratio $kang $square $fampstart $fampend $lbackcomp
[ -n "${ax0}" ] || let __lerr+=1
[ -n "${ax1}" ] || let __lerr+=1
#
if $lflag_fort13; then
ax0=0.0
ax1=0.0
cp ${fort13_jobs[${nConsidered} -1]} $sixdeskjobs_logs/fort.13
fort13_current=$sixdeskjobs_logs/fort.13
n_lines_fort13_current=$(cat $fort13_current | wc -l )
sixdeskpairs_current=$(echo $n_lines_fort13_current 15 | awk '{printf ("%.f", ($1/$2))}')
else
local __lerr=0
# returns ratio
sixdeskRatio $kang $lbackcomp
[ -n "${ratio}" ] || let __lerr+=1
# returns ax0 and ax1
sixdeskax0 $factor $beta_x $beta_x2 $beta_y $beta_y2 $ratio $kang $square $fampstart $fampend $lbackcomp
[ -n "${ax0}" ] || let __lerr+=1
[ -n "${ax1}" ] || let __lerr+=1
fi
## if fort.13 flag is on %nss will now be substituted with the number of pairs in the current fort.13 job otherwise %nss does not exist anymore
sed -e 's/%turnsl/'$turnsl'/g' \
-e 's/%ax0l/'$ax0'/g' \
-e 's/%nss/'$sixdeskpairs_current'/g' \
-e 's/%ax1l/'$ax1'/g' \
-e 's/%ratiol/'$ratio'/g' \
-e 's/%tunex/'$tunexx'/g' \
Expand Down Expand Up @@ -800,8 +855,12 @@ function submitCreateFinalInputs(){
sixdeskmess 1 "Taking care of SIXTRACK fort.2/fort.3/fort.8/fort.16 in $RundirFullPath"

# fort.3
gzip -c $sixdeskjobs_logs/fort.3 > $RundirFullPath/fort.3.gz

if $lflag_fort13;then
gzip -c $fort13_current > $RundirFullPath/fort.13.gz
gzip -c $sixdeskjobs_logs/fort.3 > $RundirFullPath/fort.3.gz
else
gzip -c $sixdeskjobs_logs/fort.3 > $RundirFullPath/fort.3.gz
fi
# input from MADX: fort.2/.8/.16
for iFort in 2 8 16 ; do
[ ! -e $RundirFullPath/fort.${iFort}.gz ] || rm -f $RundirFullPath/fort.${iFort}.gz
Expand Down Expand Up @@ -1435,9 +1494,12 @@ function treatLong(){

# separate output for current case from previous one
echo ""

sixdeskmess -1 "Considering amplitude step: $Ampl"


if $lflag_fort13;then
sixdeskmess -1 "Considering job #$Ampl from fort.13"
else
sixdeskmess -1 "Considering amplitude step: $Ampl"
fi
if ${lReduceAngsWithAmplitude}; then
jAmple=${iAmple}
else
Expand Down Expand Up @@ -1546,7 +1608,6 @@ function treatLong(){
sixdeskmess 1 "Carrying on with next WU"
continue
fi

# final preparation of all SIXTRACK files
# NB: for boinc, it returns workunitName
submitCreateFinalInputs
Expand Down Expand Up @@ -2173,7 +2234,12 @@ if ${lgenerate} || ${lfix} ; then
echo "$emit $gamma" > $sixdesktrackStudy/general_input
let __lerr+=$?
# - set up of fort.3
for tmpFile in fort.3.mad fort.3.mother1 fort.3.mother2 ; do
if $lflag_fort13; then
tmpFiles=(fort.3.mad fort.3.mother1 fort.3.mother2 fort.13)
else
tmpFiles=(fort.3.mad fort.3.mother1 fort.3.mother2)
fi
for tmpFile in ${tmpFiles[@]}; do
cp ${sixtrack_input}/${tmpFile} $sixdeskjobs_logs
if [ $? -ne 0 ] ; then
sixdeskmess -1 "unable to copy ${sixtrack_input}/${tmpFile} to $sixdeskjobs_logs"
Expand Down Expand Up @@ -2378,30 +2444,41 @@ else
sixdeskmess -1 " --> along a line in (Qx,Qy) - total: ${iTotalTunes} pairs;"
fi
fi
if [ $long -eq 1 ] ; then
# generate array of amplitudes (it returns allAmplitudeSteps, fAmpStarts, fAmpEnds, ampstart, ampfinish)
sixdeskAllAmplitudes
iTotalAmplitudeSteps=${#allAmplitudeSteps[@]}
sixdeskmess -1 "- Amplitudes: from $ns1l to $ns2l by $nsincl - total: ${iTotalAmplitudeSteps} amplitude steps;"
# generate array of angles (it returns KKs, Angles and kAngs, and KKs_ampl)
sixdeskAllAngles $kinil $kendl $kmaxl $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
iTotalAngles=${#KKs[@]}
sixdeskmess -1 "- Angles: $kinil, $kendl, $kmaxl by $kstep - total: ${iTotalAngles} angles"
if ${lReduceAngsWithAmplitude} ; then
sixdeskmess -1 " --> reduced angles with amplitude functionality active"
let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAngles}
else
let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
fi
elif [ $short -eq 1 ] || [ $da -eq 1 ] ; then
iTotalAmplitudeSteps=1
sixdeskmess -1 "- Amplitudes: from $ns1s to $ns2s by $nss - total: ${iTotalAmplitudeSteps} amplitude steps;"
# generate array of angles (it returns KKs, Angles and kAngs, and KKs_ampl)
sixdeskAllAngles $kini $kend $kmax $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
iTotalAngles=${#KKs[@]}
sixdeskmess -1 "- Angles: $kini, $kend, $kmax by $kstep - total: ${iTotalAngles} angles"
let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
fi
if [ "$lflag_fort13" = false ]; then
if [ $long -eq 1 ] ; then
# generate array of amplitudes (it returns allAmplitudeSteps, fAmpStarts, fAmpEnds, ampstart, ampfinish)
sixdeskAllAmplitudes
iTotalAmplitudeSteps=${#allAmplitudeSteps[@]}
sixdeskmess -1 "- Amplitudes: from $ns1l to $ns2l by $nsincl - total: ${iTotalAmplitudeSteps} amplitude steps;"
# generate array of angles (it returns KKs, Angles and kAngs, and KKs_ampl)
sixdeskAllAngles $kinil $kendl $kmaxl $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
iTotalAngles=${#KKs[@]}
sixdeskmess -1 "- Angles: $kinil, $kendl, $kmaxl by $kstep - total: ${iTotalAngles} angles"
if ${lReduceAngsWithAmplitude} ; then
sixdeskmess -1 " --> reduced angles with amplitude functionality active"
let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAngles}
else
let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
fi
elif [ $short -eq 1 ] || [ $da -eq 1 ] ; then
iTotalAmplitudeSteps=1
sixdeskmess -1 "- Amplitudes: from $ns1s to $ns2s by $nss - total: ${iTotalAmplitudeSteps} amplitude steps;"
# generate array of angles (it returns KKs, Angles and kAngs, and KKs_ampl)
sixdeskAllAngles $kini $kend $kmax $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
iTotalAngles=${#KKs[@]}
sixdeskmess -1 "- Angles: $kini, $kend, $kmax by $kstep - total: ${iTotalAngles} angles"
let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
sixdeskmess -1 "for a total of ${iTotal} points."
fi
else
echo "-> Flag for fort.13 input is active"
## To be changed!!
sixdeskAllAmplitudes_fort13
sixdeskAllAngles $kinil $kendl $kmaxl $kstep $ampstart $ampfinish $lbackcomp ${lReduceAngsWithAmplitude} ${totAngle} ${ampFactor}
iTotalAmplitudeSteps=${#allAmplitudeSteps[@]}
iTotalAngles=${#KKs[@]}
fi
let iTotal=${iTotalMad}*${iTotalTunes}*${iTotalAmplitudeSteps}*${iTotalAngles}
sixdeskmess -1 "for a total of ${iTotal} points."
fi

Expand Down Expand Up @@ -2430,7 +2507,11 @@ else
echo ""
sixdeskmess -1 "MADX seed $iMad"
if ${lgenerate} || ${lfix} ; then
iForts="2 8 16"
if ${lflag_fort13}; then
iForts="2 8 13 16"
else
iForts="2 8 16"
fi
if [ "$fort_34" != "" ] ; then
iForts="${iForts} 34"
fi
Expand Down
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