21 July 2025: This instance at RAL is read-only. Please do not try submitting new workflows for now.

Workflow 7666, Stage 1

Priority	50
Processors	1
Wall seconds	80000
Image	/cvmfs/singularity.opensciencegrid.org/fermilab/fnal-wn-sl7:latest
RSS bytes	2097152000 (2000 MiB)
Max distance for inputs	100.0
Enabled input RSEs	CERN_PDUNE_EOS, DUNE_CA_SFU, DUNE_CERN_EOS, DUNE_ES_PIC, DUNE_FR_CCIN2P3_DISK, DUNE_IN_TIFR, DUNE_IT_INFN_CNAF, DUNE_UK_GLASGOW, DUNE_UK_LANCASTER_CEPH, DUNE_UK_MANCHESTER_CEPH, DUNE_US_BNL_SDCC, DUNE_US_FNAL_DISK_STAGE, FNAL_DCACHE, FNAL_DCACHE_STAGING, FNAL_DCACHE_TEST, MONTECARLO, NIKHEF, PRAGUE, QMUL, RAL-PP, RAL_ECHO, SURFSARA, T3_US_NERSC
Enabled output RSEs	CERN_PDUNE_EOS, DUNE_CA_SFU, DUNE_CERN_EOS, DUNE_ES_PIC, DUNE_FR_CCIN2P3_DISK, DUNE_IN_TIFR, DUNE_IT_INFN_CNAF, DUNE_UK_GLASGOW, DUNE_UK_LANCASTER_CEPH, DUNE_UK_MANCHESTER_CEPH, DUNE_US_BNL_SDCC, DUNE_US_FNAL_DISK_STAGE, FNAL_DCACHE, FNAL_DCACHE_STAGING, FNAL_DCACHE_TEST, NIKHEF, PRAGUE, QMUL, RAL-PP, RAL_ECHO, SURFSARA, T3_US_NERSC
Enabled sites	BR_CBPF, CA_SFU, CA_Victoria, CERN, CH_UNIBE-LHEP, ES_CIEMAT, ES_PIC, FR_CCIN2P3, IN_TIFR, IT_CNAF, NL_SURFsara, UK_Bristol, UK_Brunel, UK_Durham, UK_Edinburgh, UK_Lancaster, UK_Manchester, UK_Oxford, UK_QMUL, UK_RAL-PPD, UK_RAL-Tier1, UK_Sheffield, US_Caltech, US_Colorado, US_FNAL-FermiGrid, US_FNAL-T1, US_Michigan, US_MIT, US_Nebraska, US_NotreDame, US_PuertoRico, US_SU-ITS, US_Swan, US_UChicago, US_UConn-HPC, US_UCSD, US_Wisconsin
Scope	usertests
Events for this stage

Output patterns

	Destination	Pattern	Lifetime	For next stage	RSE expression
1	https://fndcadoor.fnal.gov:2880/dune/scratch/users/calcuttj/extracted_raw/07666/1	*h5

Environment variables

Name	Value
DUNESW_TAR	/cvmfs/fifeuser2.opensciencegrid.org/sw/dune/0dfda6f3cdbf24bb65facea8e0c5f8ae2c77aa87
DUNESW_VERSION	v10_01_03d00
MCJob	1
NEVENTS	10
pipyaml	1
UNET_DIR	/cvmfs/fifeuser3.opensciencegrid.org/sw/dune/173761cb915c5a6a3193e2fafae0a8e9bcd52ebb
UTIL_TAR	/cvmfs/fifeuser1.opensciencegrid.org/sw/dune/02b48c7c914d79f401d4c55fb32fd5ebd1711857
YAMLFILE	pdhd_unet_raw.yaml

File states

Total files	Finding	Unallocated	Allocated	Outputting	Processed	Not found	Failed
100	0	0	0	0	100	0	0

Job states

Total	Submitted	Started	Processing	Outputting	Finished	Notused	Aborted	Stalled	Jobscript error	Outputting failed	None processed
394	0	0	0	0	253	0	0	122	18	0	1

RSEs used

Name	Inputs	Outputs
MONTECARLO	237	0
None	0	100

Stats of processed input files as CSV or JSON, and of uploaded output files as CSV or JSON (up to 10000 files included)

File reset events, by site

Site	Allocated	Outputting
CERN	26	0
US_UChicago	18	0
UK_RAL-Tier1	18	1
ES_PIC	15	0
US_FNAL-FermiGrid	12	0
US_Wisconsin	10	0
UK_Edinburgh	7	0
ES_CIEMAT	6	0
UK_Manchester	1	0
BR_CBPF	1	0
UK_QMUL	1	0
UK_Durham	1	1
US_PuertoRico	1	0

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

if [ -z $UNET_DIR ]; then
        echo "fatal must provide UNET_DIR env var"
        exit 1
fi

source /cvmfs/dune.opensciencegrid.org/products/dune/setup_dune.sh
setup metacat
setup python v3_9_15
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 "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
export pfn=`echo ${DID_PFN_RSE} | cut -f2 -d' '`
export did=`echo ${DID_PFN_RSE} | cut -f1 -d' '`
 

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

###Subshell for lar
#(
 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=${DUNESW_VERSION:-v10_02_02d00}
 setup dunesw \
    "${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 "printing env"
 env
 echo "DUNE specific env vars"
 env | grep DUNE

 # User can specify to pip install pyyaml
 if [ -n "$pipyaml" ]; then
   echo "Installing yaml"
   pip install --user pyyaml h5py
   echo "Done"
 # elif [ -n "${YAML_TAR}" ]; then
 #   echo "Using venv at ${YAML_TAR}"
 #   source ${YAML_TAR}/yaml_venv/bin/activate
 fi


 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 $jobid | cut -f2 -d'_'`
 fi
 nevents=${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 theyd like to use an input file or not 
 if [ -n "$MCJob" ]; then
   inputflag=""
 else
   inputflag="-i $pfn --parent $did"
 fi
 
 echo "input flag: $inputflag"
 
 # TODO -- metadata file configurable
 python -m beam_job_utils run_job \
       --json ${UTIL_TAR}/${JSONFILE:-pdsp_beam_base_meta.json} \
       --overrides ${overrides} \
       --run $run \
       --subrun $subrun \
       --yaml ${UTIL_TAR}/${YAMLFILE:-pdsp_beam_gen.yaml} \
       --nevents $nevents \
       --set_esr \
       $inputflag
 
 exitcode=$?
 if [ $exitcode -ne 0 ]; then
   echo "Error running. Exiting with ${exitcode}"
   exit $exitcode
 fi
#)

#if  [ -n $TESTFILE ]; then
#  echo $TESTFILE
#  ln -s $TESTFILE extracted.h5
#  ls -lht
#fi

export PYTHONPATH=${UNET_DIR}:${PYTHONPATH}

python -m extract -f *stage4.root \
       --input_tag "wclsnfperfect:raw" \
       --truth_tag "wclsnfperfect:raw" \
       --ranges ${UNET_DIR}/output_ranges.yaml

h5files=extracted*h5
for i in $h5files; do
  echo $i
  mv $i `echo $i | sed -e "s/\.h5/_${now}_${jobid}_${stageid}.h5/"`
done


###subshell for convert
#(
#  echo "installing torch"
#  pip install --user torch h5py
#  
#  exitcode=$?
#  if [ $exitcode -ne 0 ]; then
#    echo "Error installing torch. Exiting with ${exitcode}"
#    exit $exitcode
#  fi
#  
#  
#  ### Run convert on the output
#  #python $UNET_DIR/convert_to_pt.py extracted*h5
#  #exitcode=$?
#  #if [ $exitcode -ne 0 ]; then
#  #  echo "Error converting to torch. Exiting with ${exitcode}"
#  #  exit $exitcode
#  #fi
#  ### Run convert on the output
#  for f in `ls extracted*h5`; do
#    echo $f
#    python $UNET_DIR/convert_to_pt.py $f #$files #$pfn #extracted*h5
#    exitcode=$?
#    if [ $exitcode -ne 0 ]; then
#      echo "Error converting to torch. Exiting with ${exitcode}"
#      exit $exitcode
#    fi
#  done
#)

echo "$pfn" > justin-processed-pfns.txt