Workflow 12514, Stage 1
| Workflow | 12514 |
| Campaign | 861 |
| Priority | 50 |
| Processors | 1 |
| Wall seconds | 80000 |
| Image | /cvmfs/singularity.opensciencegrid.org/fermilab/fnal-wn-sl7:latest |
| RSS bytes | 6291456000 (6000 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, CZ_FZU, ES_CIEMAT, ES_PIC, FR_CCIN2P3, IT_CNAF, NL_NIKHEF, NL_SURFsara, UK_Bristol, UK_Brunel, UK_Durham, UK_Edinburgh, UK_Glasgow, UK_Imperial, UK_Lancaster, UK_Liverpool, UK_Manchester, UK_Oxford, UK_QMUL, UK_RAL-PPD, UK_RAL-Tier1, UK_Sheffield, US_BNL, US_Colorado, US_FNAL-FermiGrid, US_FNAL-T1, US_Michigan, US_NotreDame, US_PuertoRico, US_SU-ITS, US_Swan, US_UChicago, US_UConn-HPC, US_UCSD, US_Wisconsin |
| Scope | usertests |
| Events for this stage |
Environment variables
| Name | Value |
|---|
| INPUT_TAR_DIR_LOCAL | /cvmfs/fifeuser1.opensciencegrid.org/sw/dune/41a982918cf873372c4a4885df3a49493f8bd61a |
| NUM_EVENTS | 3 |
File states
| Total files | Finding | Unallocated | Allocated | Outputting | Processed | Not found | Failed |
|---|
|
| 3 | 0 | 3 | 0 | 0 | 0 | 0 | 0 |
Job states
| Total | Submitted | Started | Processing | Outputting | Finished | Notused | Aborted | Stalled | Jobscript error | Outputting failed | None processed |
|---|
| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Stats of processed input files as CSV or JSON, and of uploaded output files as CSV or JSON (up to 10000 files included)
Jobscript
#!/bin/bash
:<<'EOF'
To use this jobscript to process n files through the g4 stage
and put the output in pnfs scratch,
use this command to create the workflow:
justin simple-workflow \
--mql "$MQL_QUERY" \
--jobscript my-reco1.jobscript --max-distance 30 --rss-mb 4000 -- env NUM_EVENTS=10\
--scope usertests --output-pattern "*_reco_data_*.root:afm-reco1-test" --lifetime-days 1
The following optional environment variables can be set when creating the
workflow/stage: FCL_FILE, NUM_EVENTS, DUNE_VERSION, DUNE_QUALIFIER
EOF
echo "AFM reco2 jobscript."
# fcl file and DUNE software version/qualifier to be used
cp $INPUT_TAR_DIR_LOCAL/PandoraSettings_Cheating_Master_DUNEFD.xml .
cp $INPUT_TAR_DIR_LOCAL/PandoraSettings_Cheat.xml .
cp $INPUT_TAR_DIR_LOCAL/PandoraSettings_Cosmic_Cheat.xml .
cp $INPUT_TAR_DIR_LOCAL/PandoraSettings_Slicing_Cheat.xml .
FCL_FILE=${FCL_FILE:-$INPUT_TAR_DIR_LOCAL/evd_consolidated_reco.fcl}
#FCL_FILE=${FCL_FILE:-standard_reco2_dune10kt_1x2x6.fcl}
DUNE_VERSION=${DUNE_VERSION:-v10_11_00d01}
DUNE_QUALIFIER=${DUNE_QUALIFIER:-e26:prof}
# number of events to process from the input file
if [ "$NUM_EVENTS" != "" ] ; then
events_option="-n $NUM_EVENTS"
fi
# First get an unprocessed file from this stage
did_pfn_rse=`$JUSTIN_PATH/justin-get-file`
if [ "$did_pfn_rse" = "" ] ; then
echo "No input files provided."
exit 0
fi
# Keep a record of all input DIDs, for pdjson2meta file -> DID mapping
echo "$did_pfn_rse" | cut -f1 -d' ' >>all-input-dids.txt
# pfn is also needed when creating justin-processed-pfns.txt
pfn=`echo $did_pfn_rse | cut -f2 -d' '`
echo "Input PFN = $pfn" #this is the number you need to pull out the file from the list
xrdcp root://fndcadoor.fnal.gov:1094//pnfs/fnal.gov/usr/dune/scratch/users/amoor/fnal/10987/1/001/xrootdfiles.list .
input_pfn=`head -$pfn xrootdfiles.list | tail -1`
echo "input_pfn file = $input_pfn"
# Setup DUNE environment
source /cvmfs/dune.opensciencegrid.org/products/dune/setup_dune.sh
# the xroot lib for streaming non-root files is in testproducts,
# so add it to the start of the path
export PRODUCTS=/cvmfs/dune.opensciencegrid.org/products/dune/testproducts:${PRODUCTS}
setup dunesw "$DUNE_VERSION" -q "$DUNE_QUALIFIER"
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}
export FHICL_FILE_PATH=".:$FHICL_FILE_PATH"
export FW_SEARCH_PATH=".:$FW_SEARCH_PATH"
# Construct outFile from input $pfn
now=$(date -u +"%Y-%m-%dT_%H%M%SZ")
Ffname=`echo $pfn | awk -F/ '{print $NF}'`
fname=`echo $Ffname | awk -F. '{print $1}'`
outFile=${fname}_reco_data_${now}.root
campaign="justIN.w${JUSTIN_WORKFLOW_ID}s${JUSTIN_STAGE_ID}"
(
# Do the scary preload stuff in a subshell!
export LD_PRELOAD=${XROOTD_LIB}/libXrdPosixPreload.so
echo "$LD_PRELOAD"
lar -c $FCL_FILE -s $input_pfn $events_option -o $outFile "$pfn" > ${fname}_reco_${now}.log 2>&1
)
echo '=== Start last 50 lines of lar log file ==='
tail -50 ${fname}_reco_${now}.log
echo '=== End last 50 lines of lar log file ==='
# Subshell exits with exit code of last command
larExit=$?
echo "lar exit code $larExit"
jobscriptExit=1
if [ $larExit -eq 0 ] ; then
# write metadata file if lar succeeded
extractor_prod.py --infile "$outFile" --no_crc --appname reco \
--appversion ${DUNE_VERSION} --appfamily art \
--campaign ${campaign} > $outFile.ext.json
extractorExit=$?
echo "extractor_prod.py exit code $extractorExit"
# Run pdjson2meta. THIS SHOULD MOVE TO SOMEWHERE LIKE duneutil ?
/cvmfs/dune.opensciencegrid.org/products/dune/justin/pro/NULL/jobutils/pdjson2metadata \
$outFile.ext.json all-input-dids.txt > $outFile.json
p2mExit=$?
echo "pdjson2metadata exit code $p2mExit"
if [ $extractorExit -eq 0 -a $p2mExit -eq 0 ] ; then
echo "Metadata extraction succeeds"
echo "$pfn" > justin-processed-pfns.txt
echo "===Metadata JSON==="
cat $outFile.json
echo
echo "==================="
jobscriptExit=0
fi
fi
ls -lRS
# Create compressed tar file with all log files
tar zcf `echo "$JUSTIN_JOBSUB_ID.logs.tgz" | sed 's/@/_/g'` *.log
exit $jobscriptExit
