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Merged
silkenelson merged 2 commits into from
Nov 13, 2025
Merged

add epixM support to makepeds_psana2 #327

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7ec13f5
add epixM support to makepeds_psana2
silkenelson Nov 7, 2025
c12f491
fix the check for a kerberos token
silkenelson Nov 7, 2025
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122 changes: 93 additions & 29 deletions scripts/makepeds_psana2
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Original file line number Diff line number Diff line change
Expand Up @@ -43,12 +43,17 @@ OPTIONS:
write pixel mask file for pixels with pedestal above xxx )currently integer only)
-d|--calibdir
give path for alternative calibdir
-t|--test
do not deploy
--noseg
do not split jobs into segments
--gui
start calibman. -r 0: show all darks, -r n: show runs (n-25) - 25
--nstage1
events for the first stage of processing
--datinfo
print info about run for detectors

EOF
}

Expand Down Expand Up @@ -108,6 +113,12 @@ check_running_jobs()
return $NJOBS
}

get_datinfo()
{
echo DATINFO_DEBUG
datinfo -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L CRITICAL -t DRS > /tmp/datinfo_"$MYDET"_"$EXP"_"$CREATE_TIME"
}

# Arg: DETECTOR class. This could be a comma-separated list, but we're
# matching it in the config file as a string.
get_config()
Expand Down Expand Up @@ -231,6 +242,10 @@ do
shift
shift
;;
--datinfo)
DATINFO=1
shift
;;
*)
POSITIONAL+=("$1")
shift
Expand All @@ -239,11 +254,6 @@ do
done
set -- "${POSITIONAL[@]}"

#check for a valid kerberos token, otherwise the deploy step will not work!
if [ $(klist | wc -l) -eq 0 ]; then
exit 4
fi

T="$(date +%s%N)"
echo "XXXXXXXXXXXXXXXXX START MAKEPEDS at $(date +'%T') on $HOSTNAME XXXXXXXXXXXXXXXXXXXXXXXXXXXX"

Expand All @@ -263,6 +273,14 @@ MYADUMIN=${MYADUMIN:=-1}
MYADUMAX=${MYADUMAX:=-1}
#one setting to run each process on an own server (currently faster) or not (if we had to use reservations)

#check for a valid kerberos token, otherwise the deploy step will not work!
if ! klist -s ; then
echo No valid kerberos token, deployment will not work
if [ $DEPLOY == 1 ]; then
exit 4
fi
fi

if [ "$RUN" == 0 ]; then
printf "Please enter a run number HERE: \n"; read -r RUN
fi
Expand Down Expand Up @@ -442,13 +460,50 @@ if [[ $HAVE_EPIX100 -ge 1 ]]; then
echo '$MYDET is a $DETTYPE, looking for epix100'
continue
fi
echo "now calibrate $MYDET"
if [[ -v DATINFO ]]; then
echo "get information in run for ${MYDET}"
datinfo -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L CRITICAL -t DRS
fi
echo "now calibrate $MYDET"
CMD="det_dark_proc -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L INFO $LOCARG"
echo "$CMD"
$CMD
done
fi

HAVE_EPIXM=$(grep -c epixm /tmp/detnames_"$EXP"_"$CREATE_TIME")
if [[ $HAVE_EPIXM -ge 1 ]]; then
echo "***** have epixm ***"
DETNAMES=$(grep epixm /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk 'BEGIN { FS = "|"}; {print $1}' | paste -d " " -s)
for MYDET in ${DETNAMES}; do
LOCARG=$ARG' -o '$CALIBDIR
if [[ -v VALSTR ]]; then
LOCARG=$LOCARG' -t '$VALSTR
fi
if [[ -v NRECS1 ]]; then
LOCARG=$LOCARG' --nrecs1 '$NRECS1
else
LOCARG=$LOCARG' --nrecs1 100'
fi
if [[ -v NUMEVT ]]; then
LOCARG=$LOCARG' -n '$NUMEVT
fi
DETTYPE=$(grep $MYDET /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk 'BEGIN { FS = "|"}; {print $2}' | paste -d " " -s)
if [[ ! $DETTYPE =~ 'epixm' ]]; then
echo '$MYDET is a $DETTYPE, looking for epixm'
continue
fi
if [[ -v DATINFO ]]; then
echo "get information in run for $MYDET"
datinfo -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L CRITICAL -t DRS
fi
echo "now calibrate $MYDET"
CMD="epixm320_dark_proc -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L INFO $LOCARG"
echo "$CMD"
$CMD
done
fi

#DEBUG rixx1017523, run 388 : archon
#reconsider doing all det_dark_proc detectors together later
#not sure this is supported + different numbers of skip events
Expand Down Expand Up @@ -508,25 +563,30 @@ fi
HAVE_EPIX10K=$(grep -c epix10ka /tmp/detnames_"$EXP"_"$CREATE_TIME")
if [[ $HAVE_EPIX10K -ge 1 ]]; then
DETNAMES=$(grep epix10ka /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk 'BEGIN { FS = "|"}; {print $1}' | paste -d " " -s)
for EPIX10K in ${DETNAMES}; do
for MYDET in ${DETNAMES}; do
LOCARG=' -o '$CALIBDIR
#EPIX10K="${DETNAMES[i]// /}"
DETTYPE=$(grep $EPIX10K /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk 'BEGIN { FS = "|"}; {print $2}' | paste -d " " -s)
#MYDET="${DETNAMES[i]// /}"
DETTYPE=$(grep $MYDET /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk 'BEGIN { FS = "|"}; {print $2}' | paste -d " " -s)
#MYDETTYPE="${DETTYPES[i]// /}"
if [ ! "$DETTYPE" =~ 'epix10ka' ]; then
continue
fi
echo "Epix10ka name for ${EXP} is: ${EPIX10K}"
echo "Epix10ka name for ${EXP} is: ${MYDET}"

if [[ -v DATINFO ]]; then
echo "get information in run for ${MYDET}"
datinfo -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L CRITICAL -t DRS
fi
NSEG=1
if [[ $EPIX10K =~ "2M" ]]; then
if [[ $MYDET =~ "2M" ]]; then
NSEG=16;
elif [[ $EPIX10K =~ "uad" ]]; then
elif [[ $MYDET =~ "uad" ]]; then
NSEG=4;
fi
for calibcycle in {0..4}; do
nextcycle=$(( calibcycle + 1 ))
CMD="epix10ka_pedestals_calibration $LOCARG -d $EPIX10K -k exp=$EXP,run=$RUN,dir=$XTCDIR --stepnum $calibcycle --stepmax $nextcycle -L INFO"
echo "---------------EPIX10K PEDESTALS FOR CYCLE $calibcycle --------------------"
CMD="epix10ka_pedestals_calibration $LOCARG -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR --stepnum $calibcycle --stepmax $nextcycle -L INFO"
echo "---------------MYDET PEDESTALS FOR CYCLE $calibcycle --------------------"
if [[ $RUNLOCAL != 1 ]]; then
for ((segment=0; segment<NSEG; segment++)); do
if [[ $NSEG -gt 1 ]]; then
Expand All @@ -540,7 +600,7 @@ if [[ $HAVE_EPIX10K -ge 1 ]]; then
printf '#!/bin/bash\n' > "$tmpScript"
printf 'source %s/manage/bin/psconda.sh\n' "${SIT_ENV_DIR}" >> "$tmpScript"
printf '%s\n' "${CMDS}" >> "$tmpScript"
ep10kaCmd="sbatch ${SBATCH_ARGS} --mem 8GB --cpus-per-task 1 -o $WORKDIR/${EPIX10K}_${EXP}_Run${RUN}_cycle${calibcycle}_%J.out $tmpScript"
ep10kaCmd="sbatch ${SBATCH_ARGS} --mem 8GB --cpus-per-task 1 -o $WORKDIR/${MYDET}_${EXP}_Run${RUN}_cycle${calibcycle}_%J.out $tmpScript"

echo "run in queue: $ep10kaCmd"
SUBMISSION=$($ep10kaCmd)
Expand Down Expand Up @@ -586,7 +646,7 @@ if [[ $HAVE_EPIX10K -ge 1 ]]; then
fi

if [ "$DEPLOY" == 1 ]; then
echo "---------------EPIX10K PEDESTALS CALCULATED NOW DEPLOY --------------------"
echo "--------------- PEDESTALS CALCULATED NOW DEPLOY --------------------"
if [ "$NFAILEDJOBS" -gt 0 ]; then
read -r -p "$NFAILEDJOBS of the calibration tasks failed, do you want to continue anyways (y/n)?"
if [ "$REPLY" != "y" ];then
Expand All @@ -595,9 +655,9 @@ if [[ $HAVE_EPIX10K -ge 1 ]]; then
fi

for i in "${!DETNAMES[@]}"; do
EPIX10K="${DETNAMES[i]// /}"
#for EPIX10K in $DETNAMES; do
CMD="epix10ka_deploy_constants $LOCARG -D -d $EPIX10K -k exp=$EXP,run=$RUN,dir=$XTCDIR -L INFO"
MYDET="${DETNAMES[i]// /}"
#for MYDET in $DETNAMES; do
CMD="epix10ka_deploy_constants $LOCARG -D -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L INFO"
if [ -v "$VALSTR" ]; then
echo 'setting validity....'"$VALSTR"
CMD=$CMD' -t '$VALSTR
Expand Down Expand Up @@ -633,19 +693,23 @@ fi
HAVE_JUNGFRAU=$(grep -c jungfrau /tmp/detnames_"$EXP"_"$CREATE_TIME")
if [[ $HAVE_JUNGFRAU -ge 1 ]]; then
DETNAMES=$(grep jungfrau /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk 'BEGIN { FS = "|"}; {print $1}' | paste -d " " -s)
for JUNGFRAU in ${DETNAMES}; do
for MYDET in ${DETNAMES}; do
LOCARG=' -o '$CALIBDIR
DETTYPE=$(grep $JUNGFRAU /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk 'BEGIN { FS = "|"}; {print $2}' | paste -d " " -s)
DETTYPE=$(grep $MYDET /tmp/detnames_"$EXP"_"$CREATE_TIME" | grep raw | awk 'BEGIN { FS = "|"}; {print $2}' | paste -d " " -s)
if [[ ! $DETTYPE =~ 'jungfrau' ]]; then
continue
fi
echo "Jungfrau name for ${EXP} is: ${JUNGFRAU}"
echo "Jungfrau name for ${EXP} is: ${MYDET}"
if [[ -v DATINFO ]]; then
echo "get information in run for ${MYDET}"
datinfo -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L CRITICAL -t DRS
fi
NSEG=1
if [[ $JUNGFRAU =~ "16M" ]]; then
if [[ $MYDET =~ "16M" ]]; then
NSEG=32;
elif [[ $JUNGFRAU =~ "4M" ]]; then
elif [[ $MYDET =~ "4M" ]]; then
NSEG=8;
elif [[ $JUNGFRAU =~ "1M" ]]; then
elif [[ $MYDET =~ "1M" ]]; then
NSEG=2;
elif [[ $EXP =~ "mfx" ]]; then #note that this is a hotfix!
NSEG=32;
Expand All @@ -657,7 +721,7 @@ if [[ $HAVE_JUNGFRAU -ge 1 ]]; then
fi
for calibcycle in {0..2}; do
nextcycle=$(( calibcycle + 1 ))
CMD="jungfrau_dark_proc $LOCARG -d $JUNGFRAU -k exp=$EXP,run=$RUN,dir=$XTCDIR --stepnum $calibcycle --stepmax $nextcycle -L INFO"
CMD="jungfrau_dark_proc $LOCARG -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR --stepnum $calibcycle --stepmax $nextcycle -L INFO"
echo "---------------JUNGFRAU PEDESTALS FOR CYCLE $calibcycle --------------------"
if [[ $RUNLOCAL != 1 ]]; then
for ((segment=0; segment<NSEG; segment++)); do
Expand All @@ -674,7 +738,7 @@ if [[ $HAVE_JUNGFRAU -ge 1 ]]; then
printf '#!/bin/bash\n' > "$tmpScript"
printf 'source %s/manage/bin/psconda.sh\n' "${SIT_ENV_DIR}" >> "$tmpScript"
printf '%s\n' "${CMDS}" >> "$tmpScript"
jfCmd="sbatch ${SBATCH_ARGS} --mem ${MEM}GB --cpus-per-task 1 -o $WORKDIR/${JUNGFRAU}_${EXP}_Run${RUN}_cycle${calibcycle}_segment${segment}_%J.out $tmpScript"
jfCmd="sbatch ${SBATCH_ARGS} --mem ${MEM}GB --cpus-per-task 1 -o $WORKDIR/${MYDET}_${EXP}_Run${RUN}_cycle${calibcycle}_segment${segment}_%J.out $tmpScript"

echo "run in queue: $jfCmd"
SUBMISSION=$($jfCmd)
Expand Down Expand Up @@ -734,8 +798,8 @@ if [[ $HAVE_JUNGFRAU -ge 1 ]]; then
fi
fi

for JUNGFRAU in ${DETNAMES}; do
CMD="jungfrau_deploy_constants -D -d $JUNGFRAU -k exp=$EXP,run=$RUN,dir=$XTCDIR -L INFO -o $CALIBDIR -p psrnx"
for MYDET in ${DETNAMES}; do
CMD="jungfrau_deploy_constants -D -d $MYDET -k exp=$EXP,run=$RUN,dir=$XTCDIR -L INFO -o $CALIBDIR -p psrnx"
if [ -v "$VALSTR" ]; then
echo 'setting validity....'"$VALSTR"
CMD=$CMD' -t '$VALSTR
Expand Down
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