Stats of processed input files as CSV or JSON, and of uploaded output files as CSV or JSON (up to 10000 files included)
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Jobscript
#!/bin/bash
#
#These must be defined
if [ -z $UTIL_TAR ]; then
echo "Fatal must provide UTIL_TAR env var"
exit 1
fi
export PYTHONPATH=$UTIL_TAR:$PYTHONPATH
# FHICL files in tarball can be found by appending tarball to fhicl path
export FHICL_FILE_PATH=$UTIL_TAR:$FHICL_FILE_PATH
# May want to append util_tar to FW_SEARCH_PATH in the future (for data processing)
#export FW_SEARCH_PATH=$UTIL_TAR:$FW_SEARCH_PATH
source /cvmfs/dune.opensciencegrid.org/products/dune/setup_dune.sh
setup metacat
export METACAT_SERVER_URL=https://metacat.fnal.gov:9443/dune_meta_prod/app
export METACAT_AUTH_SERVER_URL=https://metacat.fnal.gov:8143/auth/dune
if [ -z ${JUSTIN_PROCESSORS} ]; then
JUSTIN_PROCESSORS=1
fi
echo "Justin processors: ${JUSTIN_PROCESSORS}"
export TF_NUM_THREADS=${JUSTIN_PROCESSORS}
export OPENBLAS_NUM_THREADS=${JUSTIN_PROCESSORS}
export JULIA_NUM_THREADS=${JUSTIN_PROCESSORS}
export MKL_NUM_THREADS=${JUSTIN_PROCESSORS}
export NUMEXPR_NUM_THREADS=${JUSTIN_PROCESSORS}
export OMP_NUM_THREADS=${JUSTIN_PROCESSORS}
echo "Justin specific env vars"
env | grep JUSTIN
now=$(date -u +"%Y%m%dT%H%M%SZ")
jobid=`echo "${JUSTIN_JOBSUB_ID:-1}" | cut -f1 -d'@' | sed -e "s/\./_/"`
stageid=${JUSTIN_STAGE_ID:-1}
a=1
if [ -n "$DUNESW_TAR" ]; then
stat ${DUNESW_TAR}
if [ $? -ne 0 ]; then
echo "Failed to stat $DUNESW_TAR. Exiting safely"
exit 0
fi
export PRODUCTS=$DUNESW_TAR:$PRODUCTS
echo "Set dunesw to $DUNESW_TAR"
fi
if [ -n "$WIRECELL_TAR" ]; then
stat ${WIRECELL_TAR}
if [ $? -ne 0 ]; then
echo "Failed to stat $WIRECELL_TAR. Exiting safely"
exit 0
fi
export PRODUCTS=$WIRECELL_TAR:$PRODUCTS
echo "Set wirecell to $WIRECELL_TAR"
fi
#Setup recent lar software suite
DUNESW_VERSION=${DUNESW_VERSION:-v10_05_00d00}
setup dunesw \
"${DUNESW_VERSION}" \
-q "${DUNE_QUALIFIER:-e26:prof}"
setup_exit=$?
if [ $? -ne 0 ]; then
echo "Failed to setup dunesw $DUNESW_VERSION $DUNE_QUALIFIER"
exit $setup_exit
fi
echo "DUNESW loc:"
ups active | grep dunesw
echo "WIRECELL loc:"
ups active | grep wirecell
echo "DUNE specific env vars"
env | grep DUNE
# User can specify to pip install pyyaml
if [ -n "$pipyaml" ]; then
echo "Installing yaml"
pip install --user pyyaml
echo "Done"
# elif [ -n "${YAML_TAR}" ]; then
# echo "Using venv at ${YAML_TAR}"
# source ${YAML_TAR}/yaml_venv/bin/activate
fi
echo "Will use justin-get-file"
DID_PFN_RSE=`$JUSTIN_PATH/justin-get-file`
if [ "${DID_PFN_RSE}" == "" ] ; then
echo "Could not get file"
exit 0
fi
pfn=`echo ${DID_PFN_RSE} | cut -f2 -d' '`
did=`echo ${DID_PFN_RSE} | cut -f1 -d' '`
input_filename=`echo $did | cut -f2 -d':'`
echo "input file: $input_filename"
echo "jobsub_id: ${JUSTIN_JOBSUB_ID:-1}"
#Get run/subrun from parent if using input -- else from justin job ID/process"
if [ -z "$MCJob" ]; then
echo "Getting run subrun from $did"
run_subrun=`python -m beam_job_utils get_run_subrun -i $did`
get_run_ret=$?
if [ $get_run_ret -ne 0 ]; then
echo "error in get_run_subrun"
fi
echo $run_subrun
run=`echo $run_subrun | cut -f1 -d' '`
subrun=`echo $run_subrun | cut -f2 -d' '`
else
run=`echo $jobid | cut -f1 -d'_'` ##TODO -- check order here
subrun=`echo $jobid | cut -f2 -d'_'`
fi
# Get correct sps spill data file for this run
#SPSDATA=$(find . -name "$UTIL_TAR/*${run}*.csv" | head -n 1)
SPSDATA=$(find "$UTIL_TAR" -type f -name "*${run}*.csv" | head -n 1)
echo "Found sps data for run ${run}: ${SPSDATA}"
# Copy the spsp spill data to job directory (one day can add it to the path)
cp $SPSDATA ./
nevents=${NEVENTS:--1} #Set from env override or -1
NSKIP=${NSKIP:-0}
echo "nevents: $nevents"
overrides="core.data_tier=full-reconstructed \
core.application.version=${DUNESW_VERSION} \
core.application.name=reco \
core.application.family=dunesw \
core.application=dunesw.reco \
"
#User specifies if they'd like to use an input file or not
if [ -n "$MCJob" ]; then
inputflag=""
else
inputflag="-i $pfn --parent $did"
fi
echo "input flag: $inputflag"
# I may need this for reading data?
export LD_PRELOAD=${XROOTD_LIB}/libXrdPosixPreload.so
# TODO -- metadata file configurable
python -m beam_job_utils run_job \
--json ${UTIL_TAR}/${JSONFILE:-pdhd_wnp04_base_meta.json} \
--overrides ${overrides} \
--run $run \
--subrun $subrun \
--yaml ${UTIL_TAR}/${YAMLFILE:-pdhd_bsmtrigger_run29424_data.yaml} \
--nevents $nevents \
--event $NSKIP \
$inputflag
exitcode=$?
if [ $exitcode -ne 0 ]; then
echo "Error running. Exiting with ${exitcode}"
exit $exitcode
fi
echo "$pfn" > justin-processed-pfns.txt
justIN time: 2025-12-19 23:03:17 UTC justIN version: 01.05.03
