condor_lar.sh

Go to the documentation of this file.

#! /bin/bash
#------------------------------------------------------------------
#
# Purpose: A general purpose larsoft batch worker script.
#
# Adapted from condor_lBdetMC.sh by E. Church.
#
# Usage:
#
# condor_lar.sh [options]
#
# Lar options:
#
# -c, --config <arg>      - Configuration (fcl) file (required).
# -s, --source <arg>      - Input file (full path).
# -S, --source-list <arg> - Input file list (full path, one per line).
# -o, --output <arg>      - Output file name.
# -T, --TFileName  <arg>  - TFile output file name
# -n, --nevts <arg>       - Number of events to process.
# --nskip <arg>           - Number of events to skip.
# --nfile <arg>           - Number of files to process per worker.
# --nfile_skip <arg>      - Number of files to skip (use with option -S).
# --inputmode <arg>       - Input mode ('textfile' or '', default '')
# --args <args...>        - Arguments for lar command line (place at end).
#
# Sam and parallel project options.
#
# --sam_user <arg>        - Specify sam user (default $GRID_USER).
# --sam_group <arg>       - Specify sam group (default --group option).
# --sam_station <arg>     - Specify sam station (default --group option).
# --sam_defname <arg>     - Sam dataset definition name.
# --sam_project <arg>     - Sam project name.
# --sam_start             - Specify that this worker should be responsible for
#                           starting and stopping the sam project.
# --recur                 - Recursive input dataset (force snapshot).
# --sam_schema <arg>      - Use this option with argument "root" to stream files using
#                           xrootd.  Leave this option out for standard file copy.
# --os <arg>              - A copy of the os argument passed to jobsub.  May be used
#                           to affect definition of UPS_OVERRIDE.
# --njobs <arg>           - Parallel project with specified number of jobs (default one).
# --data_file_type        - Specify data file type (default "root," repeatable).
#
# Mix input options (second input stream).
#
# --mix_defname <arg>     - Specify mix input sam dataset definition.
# --mix_project <arg>     - Specify mix input sam project.
#
# Validation options.
#
# --declare               - Do sam declaration.
# --validate              - Do validation checks.
# --copy                  - Copy output files directly to FTS dropbox instead of
#                           output directory.
# --maintain_parentage    - Recalculate sam parentage metadata for multistage jobs.
#                           (Use with --validate and --declare).
#
# Larsoft options.
#
# --ups <arg>             - Comma-separated list of top level run-time ups products.
# -r, --release <arg>     - Release tag.
# -q, -b, --build <arg>   - Release build qualifier (default "debug", or "prof").
# --localdir <arg>        - Larsoft local test release directory (default none).
# --localtar <arg>        - Tarball of local test release.
# --mrb                   - Ignored (for compatibility).
# --srt                   - Exit with error status (SRT run time no longer supported).
#
# Other options.
#
# -h, --help              - Print help.
# -i, --interactive       - For interactive use.
# -g, --grid              - No effect (allowed for compatibility).
# --group <arg>           - Group or experiment (required).
# --workdir <arg>         - No effect (allowed for compatibility).
# --outdir <arg>          - Output directory (required).
# --logdir <arg>          - Log directory (required).
# --dirsize <n>           - Maximum directory size.
# --dirlevels <n>         - Number of extra directory levels.
# --scratch <arg>         - Scratch directory (only for interactive).
# --cluster <arg>         - Job cluster (override $CLUSTER)
# --process <arg>         - Process within cluster (override $PROCESS).
# --procmap <arg>         - Name of process map file (override $PROCESS).
# --init-script <arg>     - User initialization script execute.
# --init-source <arg>     - User initialization script to source (bash).
# --end-script <arg>      - User end-of-job script to execute.
# --mid-source <arg>      - User midstage initialization script to source.
# --mid-script <arg>      - User midstage finalization script to execute.
# --exe <arg>             - Specify art-like executable (default "lar").
# --init <path>           - Absolute path of environment initialization script.
#
# End options.
#
# Run time environment setup.
#
# MRB run-time environmental setup is controlled by four options:
#  --release (-r), --build (-b, -q), --localdir, and --localtar.  
#
# a) Use option --release or -r to specify version of top-level product(s).  
# b) Use option --build or -b to specify build full qualifiers (e.g. 
#    "debug:e5" or "e5:prof").
# c) Options --localdir or --localtar are used to specify your local
#    test release.  Use one or the other (not both).
#
#    Use --localdir to specify the location of your local install
#    directory ($MRB_INSTALL).
#
#    Use --localtar to specify thye location of a tarball of your
#    install directory (made relative to $MRB_INSTALL).
#
#    Note that --localdir is not grid-friendly.
#
# Notes.
#
# 1.  Each batch worker is uniquely identified by two numbers stored
#     in environment variables $CLUSTER and $PROCESS (the latter is 
#     a small integer that starts from zero and varies for different
#     jobs in a parallel job group).  These environment variables are
#     normally set by the batch system, but can be overridden by options 
#     --cluster, --process, and --procmap (e.g. to rerun failed jobs).
#
# 2.  The work directory must be set to an existing directory owned
#     by the submitter and readable by the batch worker.  Files from the 
#     work directory are copied to the batch worker scratch directory at
#     the start of the job.
#
# 3.  A local test release may be specified as an absolute path using
#     --localdir, or a tarball using --localtar.  The location of the tarball
#     may be specified as an absolute path visible on the worker, or a 
#     relative path relative to the work directory.
#
# 4.  The output directory must exist and be writable by the batch
#     worker (i.e. be group-writable for grid jobs).  The worker
#     makes a new subdirectory called ${CLUSTER}_${PROCESS} in the output
#     directory and copies all files in the batch scratch directory there 
#     at the end of the job.  If the output directory is not specified, the
#     default is /grid/data/<group>/outstage/<user> (user is defined as 
#     owner of work directory).
#
# 5.  Parallel projects are specified whenever --njobs is specified to
#     be greater than one.  Parallel projects are supported for single file,
#     file list, and sam project input.
#
#     In all cases, each worker processes some number of complete files.
#     If the number of jobs is greater than the number of input files, some
#     workers will not have any input files to process.
#
#     In any case, options --nfile and --nevts can be used to limit the
#     number of files or events that are processed by a single worker, 
#     regardless of the way files are divided among the workers.
#
#     Option --njobs is incompatible with options --nskip, and --nfile_skip.
#
#     a) Non-sam (single file or file list) input.
#
#     In this case, input files are preassigned to workers such that all input
#     files are approximately evenly divided among the workers.  All files
#     preassigned to this worker are copied to the scratch directory at the 
#     start of the job.
#
#     b) Sam project input.
#
#     In this case, files are assigned to workers in a non-deterministic
#     manner by the sam system.  The sam system fetches input files to the
#     scratch directory and deletes processed input files during job execution.
#
#
# 6.  Using option -n or --nevts to limit number of events processed: 
#
#     a) If no input files are specified (e.g. mc generation), --nevts
#        specifies total number of events among all workers.
#
#     b) If input files are specified, --nevts specifies total number of 
#        events processed by each worker or from each input file, whichever
#        is less.
#
# 7.  The interactive option (-i or --interactive) allows this script
#     to be run interactively by overriding some settings that are normally
#     obtained from the batch system, including $CLUSTER, $PROCESS, and
#     the scratch directory.  Interactive jobs always set PROCESS=0 (unless
#     overridden by --process).
#
# 8. Mix options (--mix_defname, --mix_project) are only partially handled
#    in this script.  These options are parsed and their values are stored
#    in shell variables.  It is assumed that the sam project specified
#    by --mix_project has been started externally, unless --sam_start is
#    also specified, in which case this script will start the project.  
#    This script does not include any provision for joining the project.
#    Further processing of these options (joining sam project, generating
#    command line options or fcl wrappers) should be handled by user
#    provided initialization scripts (--init-script, --init-source).
#
# 9. Option --init <path> is optional.  If specified, it should point to
#    the absolute path of the experiment environment initialization script,
#    which path must be visible from the batch worker (e.g. /cvmfs/...).
#    If this option is not specified, this script will look for and source
#    a script with hardwired name "setup_experiment.sh" in directory
#    ${CONDIR_DIR_INPUT}.
#
#
# Created: H. Greenlee, 29-Aug-2012
#
#------------------------------------------------------------------

# Parse arguments.

FCL=""
INFILE=""
INLIST=""
INMODE=""
OUTFILE=""
TFILE=""
NEVT=0
NSKIP=0
SUBRUN=1
NFILE=0
NFILE_SKIP=0
NJOBS=1
ARGS=""
UPS_PRDS=""
REL=""
QUAL=""
LOCALDIR=""
LOCALTAR=""
INTERACTIVE=0
GRP=""
OUTDIR=""
LOGDIR=""
DIRSIZE=0
DIRLEVELS=0
SCRATCH=""
CLUS=""
PROC=""
PROCMAP=""
INITSCRIPT=""
INITSOURCE=""
ENDSCRIPT=""
MIDSOURCE=""
MIDSCRIPT=""
SAM_USER=$GRID_USER
SAM_GROUP=""
SAM_STATION=""
SAM_DEFNAME=""
SAM_PROJECT=""
SAM_START=0
RECUR=0
SAM_SCHEMA=""
OS=""
USE_SAM=0
MIX_DEFNAME=""
MIX_PROJECT=""
MIX_SAM=0
IFDH_OPT=""
DECLARE_IN_JOB=0
VALIDATE_IN_JOB=0
COPY_TO_FTS=0
MAINTAIN_PARENTAGE=0
EXE="lar"
INIT=""
declare -a DATAFILETYPES

while [ $# -gt 0 ]; do
  case "$1" in

    # Help.
    -h|--help )
      awk '/^# Usage:/,/^# End options/{print $0}' $0 | cut -c3- | head -n -2
      exit
      ;;

    # Config file.
    -c|--config )
      if [ $# -gt 1 ]; then
        FCL=$2
        shift
      fi
      ;;

    # Input file.
    -s|--source )
      if [ $# -gt 1 ]; then
        INFILE=$2
        shift
      fi
      ;;

    # Input file list.
    -S|--source-list )
      if [ $# -gt 1 ]; then
        INLIST=$2
        shift
      fi
      ;;

    # Input file mode.
    --inputmode )
      if [ $# -gt 1 ]; then
        INMODE=$2
        shift
      fi
      ;;

    # Output file.
    -o|--output )
      if [ $# -gt 1 ]; then
        OUTFILE=$2
        shift
      fi
      ;;
      
    # Output TFile.
    -T|--TFileName )
      if [ $# -gt 1 ]; then
        TFILE=$2
        shift
      fi
      ;;    

    # Number of events.
    -n|--nevts )
      if [ $# -gt 1 ]; then
        NEVT=$2
        shift
      fi
      ;;

    # Number of events to skip.
    --nskip )
      if [ $# -gt 1 ]; then
        NSKIP=$2
        shift
      fi
      ;;

    # Number of files to process.
    --nfile )
      if [ $# -gt 1 ]; then
        NFILE=$2
        shift
      fi
      ;;

    # Number of files to skip.
    --nfile_skip )
      if [ $# -gt 1 ]; then
        NFILE_SKIP=$2
        shift
      fi
      ;;

    # Number of parallel jobs.
    --njobs )
      if [ $# -gt 1 ]; then
        NJOBS=$2
        shift
      fi
      ;;

    # Specify data file types (repeatable).
    --data_file_type )
      if [ $# -gt 1 ]; then
        ntype=${#DATAFILETYPES[@]}
        DATAFILETYPES[$ntype]=$2
        shift
      fi
      ;;

    # Sam user.
    --sam_user )
      if [ $# -gt 1 ]; then
        SAM_USER=$2
        shift
      fi
      ;;

    # Sam group.
    --sam_group )
      if [ $# -gt 1 ]; then
        SAM_GROUP=$2
        shift
      fi
      ;;

    # Sam station.
    --sam_station )
      if [ $# -gt 1 ]; then
        SAM_STATION=$2
        shift
      fi
      ;;

    # Sam dataset definition name.
    --sam_defname )
      if [ $# -gt 1 ]; then
        SAM_DEFNAME=$2
        USE_SAM=1
        shift
      fi
      ;;

    # Sam project name.
    --sam_project )
      if [ $# -gt 1 ]; then
        SAM_PROJECT=$2
        USE_SAM=1
        shift
      fi
      ;;

    # Sam start/stop project flag.
    --sam_start )
      SAM_START=1
      ;;

    # Recursive flag.
    --recur )
      RECUR=1
      ;;

    # Sam schema.
    --sam_schema )
      if [ $# -gt 1 ]; then
        SAM_SCHEMA=$2
        shift
      fi
      ;;

    # OS.
    --os )
      if [ $# -gt 1 ]; then
        OS=$2
        shift
      fi
      ;;

    # General arguments for lar command line.
    --args )
      if [ $# -gt 1 ]; then
        shift
        ARGS=$@
        break
      fi
      ;;

    # Top level ups products (comma-separated list).
    --ups )
      if [ $# -gt 1 ]; then
        UPS_PRDS=$2
        shift
      fi
      ;;

    # Release tag.
    -r|--release )
      if [ $# -gt 1 ]; then
        REL=$2
        shift
      fi
      ;;

    # Release build qualifier.
    -q|-b|--build )
      if [ $# -gt 1 ]; then
        QUAL=$2
        shift
      fi
      ;;

    # Local test release directory.
    --localdir )
      if [ $# -gt 1 ]; then
        LOCALDIR=$2
        shift
      fi
      ;;

    # Local test release tarball.
    --localtar )
      if [ $# -gt 1 ]; then
        LOCALTAR=$2
        shift
      fi
      ;;

    # MRB flag.
    --mrb )
      ;;

    # SRT flag.
    --srt )
      echo "SRT run time environment is no longer supported."
      exit 1
      ;;

    # Interactive flag.
    -i|--interactive )
      INTERACTIVE=1
      ;;

    # Grid flag (no effect).
    -g|--grid )
      ;;

    # Group.
    --group )
      if [ $# -gt 1 ]; then
        GRP=$2
        shift
      fi
      ;;

    # Work directory.
    --workdir )
      if [ $# -gt 1 ]; then
        shift
      fi
      ;;

    # Output directory.
    --outdir )
      if [ $# -gt 1 ]; then
        OUTDIR=$2
        shift
      fi
      ;;

    # Log directory.
    --logdir )
      if [ $# -gt 1 ]; then
        LOGDIR=$2
        shift
      fi
      ;;

    # Maximum directory size.
    --dirsize )
      if [ $# -gt 1 ]; then
        DIRSIZE=$2
        shift
      fi
      ;;

    # Number of extra directory levels.
    --dirlevels )
      if [ $# -gt 1 ]; then
        DIRLEVELS=$2
        shift
      fi
      ;;

    # Scratch directory.
    --scratch )
      if [ $# -gt 1 ]; then
        SCRATCH=$2
        shift
      fi
      ;;

    # Job cluster.
    --cluster )
      if [ $# -gt 1 ]; then
        CLUS=$2
        shift
      fi
      ;;

    # Process within cluster.
    --process )
      if [ $# -gt 1 ]; then
        PROC=$2
        shift
      fi
      ;;

    # Process map.
    --procmap )
      if [ $# -gt 1 ]; then
        PROCMAP=$2
        shift
      fi
      ;;

    # User initialization script.
    --init-script )
      if [ $# -gt 1 ]; then
        INITSCRIPT=$2
        shift
      fi
      ;;

    # User source initialization script.
    --init-source )
      if [ $# -gt 1 ]; then
        INITSOURCE=$2
        shift
      fi
      ;;

    # User end-of-job script.
    --end-script )
      if [ $# -gt 1 ]; then
        ENDSCRIPT=$2
        shift
      fi
      ;;
    
    # User midstage initialization source script.
    --mid-source )
      if [ $# -gt 1 ]; then
        MIDSOURCE=$2
        shift
      fi
      ;;
    
    # User midstage finalization script.
    --mid-script )
      if [ $# -gt 1 ]; then
        MIDSCRIPT=$2
        shift
      fi
      ;;
    
    # Declare good output root files to SAM.
    --declare )
      DECLARE_IN_JOB=1
      ;;
      
    # Run validation steps in project.py on root outputs directly in the job.
    --validate )
      VALIDATE_IN_JOB=1
      ;;

   # Copy Output to FTS.
    --copy )
      COPY_TO_FTS=1
      ;;

    # Mix input sam dataset.
    --mix_defname )
      if [ $# -gt 1 ]; then
        MIX_DEFNAME=$2
        MIX_SAM=1
        shift
      fi
      ;;

    # Mix input sam project.
    --mix_project )
      if [ $# -gt 1 ]; then
        MIX_PROJECT=$2
        MIX_SAM=1
        shift
      fi
      ;;

    # Alter the output file's parentage such that it's parent(s) are from the input list OR sam process
    --maintain_parentage )
      MAINTAIN_PARENTAGE=1
      ;;  
    
    # Specify alternate art-like executable.
    --exe )
      if [ $# -gt 1 ]; then
        EXE=$2
        shift
      fi
      ;;

    # Specify environment initialization script path.
    --init )
      if [ $# -gt 1 ]; then
        INIT=$2
        shift
      fi
      ;;

    # Other.
    * )
      echo "Unknown option $1"
      exit 1
  esac
  shift
done

#echo "FCL=$FCL"
#echo "INFILE=$INFILE"
#echo "INLIST=$INLIST"
#echo "OUTFILE=$OUTFILE"
#echo "TFILE=$TFILE"
#echo "NEVT=$NEVT"
#echo "NSKIP=$NSKIP"
#echo "NFILE=$NFILE"
#echo "NFILE_SKIP=$NFILE_SKIP"
#echo "NJOBS=$NJOBS"
#echo "ARGS=$ARGS"
#echo "REL=$REL"
#echo "QUAL=$QUAL"
#echo "LOCALDIR=$LOCALDIR"
#echo "LOCALTAR=$LOCALTAR"
#echo "INTERACTIVE=$INTERACTIVE"
#echo "GRP=$GRP"
#echo "OUTDIR=$OUTDIR"
#echo "LOGDIR=$LOGDIR"
#echo "SCRATCH=$SCRATCH"
#echo "CLUS=$CLUS"
#echo "PROC=$PROC"
#echo "INITSCRIPT=$INITSCRIPT"
#echo "INITSOURCE=$INITSOURCE"
#echo "ENDSCRIPT=$ENDSCRIPT"
#echo "MIDSOURCE=$MIDSOURCE"
#echo "MIDSCRIPT=$MIDSCRIPT"
#echo "VALIDATE_IN_JOB=$VALIDATE_IN_JOB"

# Set default data file types ("root").

if [ ${#DATAFILETYPES[@]} -eq 0 ]; then
  DATAFILETYPES[0]=root
fi

# Done with arguments.

echo "Nodename: `hostname -f`"
id
echo "Load average:"
cat /proc/loadavg

# Set defaults.

if [ x$QUAL = x ]; then
  QUAL="prof:e9"
fi

if [ x$SAM_GROUP = x ]; then
  SAM_GROUP=$GRP
fi

if [ x$SAM_STATION = x ]; then
  SAM_STATION=$GRP
fi

# Standardize sam_schema (xrootd -> root, xroot -> root).

if [ x$SAM_SCHEMA = xxrootd ]; then
  SAM_SCHEMA=root
fi
if [ x$SAM_SCHEMA = xxroot ]; then
  SAM_SCHEMA=root
fi

# Fix for sites with newer linux kernels:
# Do this only if OS is exclusively requested as SL6.

#if [ x$OS = xSL6 ]; then
#  case `uname -r` in
#    3.*) export UPS_OVERRIDE="-H Linux64bit+2.6-2.12";;
#    4.*) export UPS_OVERRIDE="-H Linux64bit+2.6-2.12";;
#  esac
#fi
echo "uname -r: `uname -r`"
echo "UPS_OVERRIDE: $UPS_OVERRIDE"

echo "Condor dir input: $CONDOR_DIR_INPUT"

# Initialize experiment ups products and mrb.

echo "Initializing ups and mrb."

if [ x$INIT != x ]; then
  if [ ! -f $INIT ]; then
    echo "Environment initialization script $INIT not found."
    exit 1
  fi
  echo "Sourcing $INIT"
  source $INIT
else
  echo "Sourcing setup_experiment.sh"
  source ${CONDOR_DIR_INPUT}/setup_experiment.sh
fi

echo PRODUCTS=$PRODUCTS
echo "ups flavor: `ups flavor`"

# Set GROUP environment variable.

unset GROUP
if [ x$GRP != x ]; then
  GROUP=$GRP
else
  echo "GROUP not specified."
  exit 1  
fi
export GROUP
echo "Group: $GROUP"

# Set options for ifdh.

echo "X509_USER_PROXY = $X509_USER_PROXY"
echo "IFDH_OPT=$IFDH_OPT"

# Make sure fcl file argument was specified.

if [ x$FCL = x ]; then
  echo "No configuration option (-c|--config) was specified."
  exit 1
fi

# Make sure output directory exists and is writable.

if [ x$OUTDIR = x ]; then
  echo "Output directory not specified."
  exit 1
fi
echo "Output directory: $OUTDIR"

# Make sure log directory exists and is writable.

if [ x$LOGDIR = x ]; then
  echo "Log directory not specified."
  exit 1
fi
echo "Log directory: $LOGDIR"

# Make sure scratch directory is defined.
# For batch, the scratch directory is always $_CONDOR_SCRATCH_DIR
# For interactive, the scratch directory is specified by option 
# --scratch or --outdir.

if [ $INTERACTIVE -eq 0 ]; then
  SCRATCH=$_CONDOR_SCRATCH_DIR
else
  if [ x$SCRATCH = x ]; then
    SCRATCH=$OUTDIR
  fi
fi
if [ x$SCRATCH = x -o ! -d "$SCRATCH" -o ! -w "$SCRATCH" ]; then
  echo "Local scratch directory not defined or not writable."
  exit 1
fi

# Create the scratch directory in the condor scratch diretory.
# Copied from condor_lBdetMC.sh.
# Scratch directory path is stored in $TMP.
# Scratch directory is automatically deleted when shell exits.

# Do not change this section.
# It creates a temporary working directory that automatically cleans up all
# leftover files at the end.
TMP=`mktemp -d ${SCRATCH}/working_dir.XXXXXXXXXX`
TMP=${TMP:-${SCRATCH}/working_dir.$$}

{ [[ -n "$TMP" ]] && mkdir -p "$TMP"; } || \
  { echo "ERROR: unable to create temporary directory!" 1>&2; exit 1; }
trap "[[ -n \"$TMP\" ]] && { rm -rf \"$TMP\"; }" 0
chmod 755 $TMP
cd $TMP
# End of the section you should not change.

echo "Scratch directory: $TMP"

# Copy files from work directory to scratch directory.

echo "No longer fetching files from work directory."
echo "that's now done with using jobsub -f commands"
mkdir work
cp ${CONDOR_DIR_INPUT}/* ./work/
cd work
find . -name \*.tar -exec tar xf {} \;
find . -name \*.py -exec chmod +x {} \;
find . -name \*.sh -exec chmod +x {} \;
echo "Local working directoroy:"
pwd
ls
echo

# Save the hostname and condor job id.

hostname > hostname.txt
echo ${CLUSTER}.${PROCESS} > jobid.txt

# Set default CLUSTER and PROCESS environment variables for interactive jobs.

if [ $INTERACTIVE -ne 0 ]; then
  CLUSTER=`date +%s`   # From time stamp.
  PROCESS=0            # Default zero for interactive.
fi

# Override CLUSTER and PROCESS from command line options.

if [ x$CLUS != x ]; then
  CLUSTER=$CLUS
fi
if [ x$PROC != x ]; then
  PROCESS=$PROC
fi
if [ x$PROCMAP != x ]; then
  if [ -f $PROCMAP ]; then
    PROCESS=`sed -n $(( $PROCESS + 1 ))p $PROCMAP`
  else
    echo "Process map file $PROCMAP not found."
    exit 1
  fi
fi
if [ x$CLUSTER = x ]; then
  echo "CLUSTER not specified."
  exit 1
fi
if [ x$PROCESS = x ]; then
  echo "PROCESS not specified."
  exit 1
fi
echo "Procmap: $PROCMAP"
echo "Cluster: $CLUSTER"
echo "Process: $PROCESS"

# Construct name of output subdirectory.

parentdir=''
ndir=$PROCESS
while [ $DIRLEVELS -gt 0 -a $DIRSIZE -gt 0 ]; do
  parentdir=$(( $ndir % $DIRSIZE ))/$parentdir
  ndir=$(( $ndir / $DIRSIZE ))
  DIRLEVELS=$(( $DIRLEVELS - 1 ))
done
OUTPUT_SUBDIR=${parentdir}${CLUSTER}_${PROCESS}
echo "Output subdirectory: $OUTPUT_SUBDIR"

# Make sure fcl file exists.

if [ ! -f $FCL ]; then
  echo "Configuration file $FCL does not exist."
  exit 1
fi

# Make sure init script exists and is executable (if specified).

if [ x$INITSCRIPT != x ]; then
  if [ -f "$INITSCRIPT" ]; then
    chmod +x $INITSCRIPT
  else
    echo "Initialization script $INITSCRIPT does not exist."
    exit 1
  fi
fi

# Make sure init source script exists (if specified).

if [ x$INITSOURCE != x -a ! -f "$INITSOURCE" ]; then
  echo "Initialization source script $INITSOURCE does not exist."
  exit 1
fi

# Make sure end-of-job script exists and is executable (if specified).

if [ x$ENDSCRIPT != x ]; then
  if [ -f "$ENDSCRIPT" ]; then
    chmod +x $ENDSCRIPT
  else
    echo "Finalization script $ENDSCRIPT does not exist."
    exit 1
  fi
fi

# Make sure midstage init source script exists (if specified).

if [ x$MIDSOURCE != x -a ! -f "$MIDSOURCE" ]; then
  echo "Midstage initialization source script $MIDSOURCE does not exist."
  exit 1
fi

# Make sure midstage finalization script exists and is executable (if specified).

if [ x$MIDSCRIPT != x ]; then
  if [ -f "$MIDSCRIPT" ]; then
    chmod +x $MIDSCRIPT
  else
    echo "Midstage finalization script $MIDSCRIPT does not exist."
    exit 1
  fi
fi

# MRB run time environment setup goes here.

# Setup local test release, if any.

if [ x$LOCALDIR != x ]; then
  mkdir $TMP/local
  cd $TMP/local

  # Copy test release directory recursively.

  echo "Copying local test release from directory ${LOCALDIR}."

  # Make sure ifdhc is setup.

  if [ x$IFDHC_DIR = x ]; then
    echo "Setting up ifdhc before fetching local directory."
    setup ifdhc
  fi
  echo "IFDHC_DIR=$IFDHC_DIR"
  ifdh cp -r $IFDH_OPT $LOCALDIR .
  stat=$?
  if [ $stat -ne 0 ]; then
    echo "ifdh cp failed with status ${stat}."
    exit $stat
  fi
  find . -name \*.py -exec chmod +x {} \;
  find . -name \*.sh -exec chmod +x {} \;

  # Setup the environment.

  cd $TMP/work
  echo "Initializing localProducts from ${LOCALDIR}."
  if [ ! -f $TMP/local/setup ]; then
    echo "Local test release directory $LOCALDIR does not contain a setup script."
    exit 1
  fi
  sed "s@setenv MRB_INSTALL.*@setenv MRB_INSTALL ${TMP}/local@" $TMP/local/setup | \
  sed "s@setenv MRB_TOP.*@setenv MRB_TOP ${TMP}@" > $TMP/local/setup.local

  # Make sure we have the correct version of mrb setup 

  if grep -q bin/shell_independence $TMP/local/setup.local; then

    # This is an old style working area.
    # Set up old version of mrb.

    echo "Setting up old version of mrb."
    unsetup mrb
    setup mrb -o
  fi

  # Do local setup

  . $TMP/local/setup.local
  #echo "MRB_INSTALL=${MRB_INSTALL}."
  #echo "MRB_QUALS=${MRB_QUALS}."
  #echo "Setting up all localProducts."
  #if [ x$IFDHC_DIR != x ]; then
  #  unsetup ifdhc
  #fi
  #mrbslp
fi
cd $TMP/work

# Setup local larsoft test release from tarball.

if [ x$LOCALTAR != x ]; then
  mkdir $TMP/local
  cd $TMP/local

  # Fetch the tarball.

  echo "Fetching test release tarball ${LOCALTAR}."

  # Make sure ifdhc is setup.

  if [ x$IFDHC_DIR = x ]; then
    echo "Setting up ifdhc before fetching tarball."
    setup ifdhc
  fi
  echo "IFDHC_DIR=$IFDHC_DIR"
  ifdh cp $LOCALTAR local.tar
  stat=$?
  if [ $stat -ne 0 ]; then
    echo "ifdh cp failed with status ${stat}."
    exit $stat
  fi 

  # Extract the tarball.

  tar -xf local.tar

  # Setup the environment.

  cd $TMP/work
  echo "Initializing localProducts from tarball ${LOCALTAR}."
  sed "s@setenv MRB_INSTALL.*@setenv MRB_INSTALL ${TMP}/local@" $TMP/local/setup | \
  sed "s@setenv MRB_TOP.*@setenv MRB_TOP ${TMP}@" > $TMP/local/setup.local

  # Make sure we have the correct version of mrb setup 

  if grep -q bin/shell_independence $TMP/local/setup.local; then

    # This is an old style working area.
    # Set up old version of mrb.

    echo "Setting up old version of mrb."
    unsetup mrb
    setup mrb -o
  fi

  # Do local setup

  . $TMP/local/setup.local
  #echo "MRB_INSTALL=${MRB_INSTALL}."
  #echo "MRB_QUALS=${MRB_QUALS}."
  #echo "Setting up all localProducts."
  #if [ x$IFDHC_DIR != x ]; then
  #  unsetup ifdhc
  #fi
  #mrbslp
fi

# Setup specified version of top level run time products
# (if specified, and if local test release did not set them up).

for prd in `echo $UPS_PRDS | tr , ' '`
do
  if ! ups active | grep -q $prd; then
    echo "Setting up $prd $REL -q ${QUAL}."
    if [ x$IFDHC_DIR != x -a x$IFBEAM_DIR = x ]; then
      unsetup ifdhc
    fi
    setup $prd $REL -q $QUAL
  fi
done

ups active

cd $TMP/work

# In case mrb setup didn't setup a version of ifdhc, set up ifdhc again.

if [ x$IFDHC_DIR = x ]; then
  echo "Setting up ifdhc again, because larsoft did not set it up."
  setup ifdhc
fi
echo "IFDH_ART_DIR=$IFDH_ART_DIR"
echo "IFDHC_DIR=$IFDHC_DIR"

# Run/source optional initialization scripts.

if [ x$INITSCRIPT != x ]; then
  echo "Running initialization script ${INITSCRIPT}."
  ./${INITSCRIPT}
  status=$?
  if [ $status -ne 0 ]; then
    exit $status
  fi
fi

if [ x$INITSOURCE != x ]; then
  echo "Sourcing initialization source script ${INITSOURCE}."
  . $INITSOURCE
  status=$?
  if [ $status -ne 0 ]; then
    exit $status
  fi
fi

# Save a copy of the environment, which can be helpful for debugging.

env > env.txt

# Get input files to process, either single file, file list, or sam.
#
# For non-sam non-xrootd input, copy all files local using ifdh cp, and make a 
# local file list called condor_lar_input.list.  Save the remote file names (uri's)
# in another file called transferred_uris.list
#
# For non-sam xrootd input ("--sam_schema root") convert input list to xrootd uri's,
# if possible.

rm -f condor_lar_input.list
rm -f transferred_uris.list
NFILE_TOTAL=0
parent_files=()
aunt_files=() #for data overaly, the data files being brought in are the output's aunts. 

if [ $USE_SAM -eq 0 -a x$INFILE != x ]; then

  # Single file case.

  # Don't allow any list-related options in single file case:
  # -S, --source-list, --nfile, --nfile_skip

  if [ x$INLIST != x -o $NFILE -ne 0 -o $NFILE_SKIP -ne 0 ]; then
    echo "File list options specified with single input file."
    exit 1
  fi

  #set the parent file to be the input file
  parent_files=("${parent_files[@]}" $INFILE)

  # Copy input file to scratch directoroy or convert to xrootd url.

  NFILE_TOTAL=1
  XROOTD_URI=$INFILE
  if [ x$SAM_SCHEMA = xroot ]; then
    XROOTD_URI=`file_to_url.sh $INFILE`
  fi
  if [ $XROOTD_URI != $INFILE ]; then
    echo $INFILE > transferred_uris.list
    echo $XROOTD_URI > condor_lar_input.list
    echo "Input xrootd uri: $XROOTD_URI"
  else
    LOCAL_INFILE=`basename $INFILE`
    echo "Copying $INFILE"
    ifdh cp $INFILE $LOCAL_INFILE
    stat=$?
    if [ $stat -ne 0 ]; then
      echo "ifdh cp failed with status ${stat}."
      exit $stat
    fi 
    if [ -f $LOCAL_INFILE -a $stat -eq 0 ]; then
      echo $INFILE > transferred_uris.list
      echo $LOCAL_INFILE > condor_lar_input.list
    else
      echo "Error fetching input file ${INFILE}."
      exit 1
    fi
  fi

elif [ $USE_SAM -eq 0 -a x$INLIST != x ]; then

  # Input list case.

  # Make sure input file list exists.

  if [ ! -f $INLIST ]; then
    echo "Input file list $INLIST does not exist."
    exit 1
  fi

  # Remember how many files are in the input file list.

  NFILE_TOTAL=`cat $INLIST | wc -l`
  echo "Input file list contains $NFILE_TOTAL total files."

  # Clamp the total number of files to be a maximum of NFILE * NJOBS, where
  # NFILE and NJOBS are specified via command line options.  In project.py
  # terms, NFILE is <maxfilesperjob> and NOJBS is <numjobs>.

  MAX_TOTAL=$(( $NFILE * $NJOBS ))
  if [ $MAX_TOTAL -gt 0 -a $NFILE_TOTAL -gt $MAX_TOTAL ]; then
    NFILE_TOTAL=$MAX_TOTAL
    echo "Number of files to be processed will be limited to ${NFILE_TOTAL}."
  fi

  # If --njobs was specified, calculate how many files
  # to skip and process in this worker.

  if [ $NJOBS -ne 0 ]; then

    # Don't allow option --nfile_skip in this case.

    if [ $NFILE_SKIP -ne 0 ]; then
      echo "Illegal options specified with --njobs."
      exit 1
    fi

    # Clamp NJOBS to be a maximum of $NFILE_TOTAL.
    # This means that workers with $PROCESS >= $NFILE_TOTAL will not have 
    # any input files to process.

    MYNJOBS=$NJOBS
    if [ $MYNJOBS -gt $NFILE_TOTAL ]; then
      MYNJOBS=$NFILE_TOTAL
    fi

    # Calculate number of files to skip and number of files to process.

    NFILE_SKIP=$(( $PROCESS * $NFILE_TOTAL / $MYNJOBS ))
    MYNFILE=$(( ( $PROCESS + 1 ) * $NFILE_TOTAL / $MYNJOBS - $NFILE_SKIP ))
    if [ $MYNFILE -eq 0 -o $NFILE_SKIP -ge $NFILE_TOTAL ]; then
      echo "This worker did not get any input files."
      exit 1
    fi
    if [ $MYNFILE -lt $NFILE -o $NFILE -eq 0 ]; then
      NFILE=$MYNFILE
    fi
  fi

  # Report number of files to skip and process.

  echo "Skipping $NFILE_SKIP files."
  if [ $NFILE -eq 0 ]; then
    echo "Processing all remaining files."
  else
    echo "Processing $NFILE files."
  fi

  # Copy input files and construct local input file list.

  nfile=0
  nfskip=$NFILE_SKIP
  nmax=$NFILE
  while read infile; do
    if [ $nfskip -gt 0 ]; then
      nfskip=$(( $nfskip - 1 ))
    else

      # Retain the original file name as the local file name, if possible.
      # Otherwise, generate a new (hopefully) unique name.

      if [ ! -f condor_lar_input.list ]; then
        touch condor_lar_input.list
      fi

      XROOTD_URI=$infile
      if [ x$SAM_SCHEMA = xroot ]; then
        XROOTD_URI=`file_to_url.sh $infile`
      fi
      if [ $XROOTD_URI != $infile ]; then
        echo $infile >> transferred_uris.list
        echo $XROOTD_URI >> condor_lar_input.list
        echo "Input xrootd uri: $XROOTD_URI"
      else
        LOCAL_INFILE=`basename $infile`
        if grep -q $LOCAL_INFILE condor_lar_input.list; then
          LOCAL_INFILE=input${nfile}.root
          if [ "$INMODE" = 'textfile' ]; then
            LOCAL_INFILE=input${nfile}.txt
          fi
        fi
        echo "Copying $infile"
        ifdh cp $infile $LOCAL_INFILE
        stat=$?
        if [ $stat -ne 0 ]; then
          echo "ifdh cp failed with status ${stat}."
          exit $stat
        fi
        if [ -f $LOCAL_INFILE -a $stat -eq 0 ]; then
          echo $infile >> transferred_uris.list
          echo $LOCAL_INFILE >> condor_lar_input.list
          parent_files=("${parent_files[@]}" $LOCAL_INFILE)
        else
          echo "Error fetching input file ${infile}."
          exit 1
        fi
      fi
      nmax=$(( $nmax - 1 ))
      if [ $nmax -eq 0 ]; then
        break
      fi
    fi
    nfile=$(( $nfile + 1 ))
  done < $INLIST
fi

NFILE_LOCAL=0
if [ $USE_SAM -eq 0 -a x$SAM_SCHEMA != xroot ]; then
  if [ -f condor_lar_input.list ]; then

    # Sort input list by decreasing size so we don't get a file with
    # zero events as the first file.

    #ls -S1 `cat condor_lar_input.list` > condor_lar_input.list
    xargs ls -s1 < condor_lar_input.list | sort -nr | awk '{print $2}' > newcondor_lar_input.list
    mv -f newcondor_lar_input.list condor_lar_input.list
    echo "Local input file list:"
    cat condor_lar_input.list
    NFILE_LOCAL=`cat condor_lar_input.list | wc -l`
  else
    echo "No local input files."
  fi
  echo "Local input list has $NFILE_LOCAL files."
fi

#Break the master wrapper fcl into each stage
nfcls=0

while read -r line
do

  if [ "$(echo $line | awk '{print $1}')" = "#---STAGE" ]; then
    stage="$(echo $line | awk '{print $2}')"
    stage_fcl="Stage$stage.fcl"
    nfcls=$(( $nfcls + 1 )) 
    continue
  fi

  if [ "$line" = "#---END_STAGE" ]; then
     #cat EOF >> $fcl
    continue
  fi
  echo $line >> $stage_fcl
done < $FCL

#We now have nStage fcl files, each which need to be run serially 
stage=0

echo "Start loop over stages"
while [ $stage -lt $nfcls ]; do
  FCL="Stage$stage.fcl"
 
  # In case no input files were specified, and we are not getting input
  # from sam (i.e. mc generation), recalculate the subrun number, and the 
  # number of events to generate in this worker.
  # This also applies to the textfile inputmode.
  # Note this only applies to the first stage by definition
 
  if [ $stage -eq 0 -a $USE_SAM -eq 0 ] && [ $NFILE_TOTAL -eq 0 -o "$INMODE" = 'textfile' ]; then #need to ask what is going on here


    # Don't allow --nskip.

    if [ $NSKIP -gt 0 ]; then
      echo "Illegal option --nskip specified with no input."
      exit 1
    fi

    # Do calculation.

    NSKIP=$(( $PROCESS * $NEVT / $NJOBS ))
    NEV=$(( ( $PROCESS + 1 ) * $NEVT / $NJOBS - $NSKIP ))
    NSKIP=0
    NEVT=$NEV

    # Set subrun=$PROCESS+1 in a wrapper fcl file.

    SUBRUN=$(( $PROCESS + 1))
    cat <<EOF > subrun_wrapper.fcl
#include "$FCL"  

source.firstSubRun: $SUBRUN

EOF
    if [ "$INMODE" = 'textfile' ]; then
    
      if [ $NFILE_LOCAL -ne 1 ]; then
        echo "Text file input mode specified with wrong number of input files."
        exit 1
      fi
      echo "physics.producers.generator.InputFileName: \"`cat condor_lar_input.list`\"" >> subrun_wrapper.fcl
    fi
  
    FCL=subrun_wrapper.fcl
  
    echo "MC subrun: $SUBRUN"
    echo "Number of MC events: $NEVT"
 
  fi

  # Sam stuff for main input.

  PURL=''
  CPID=''
  if [ $USE_SAM -ne 0 -a $stage -eq 0 ]; then
    echo "In SAM if" 

    # Make sure a project name has been specified.

    if [ x$SAM_PROJECT = x ]; then
      echo "No sam project was specified."
      exit 1
    fi
    echo "Sam project: $SAM_PROJECT"

    # Start project (if requested).

    if [ $SAM_START -ne 0 ]; then
      if [ x$SAM_DEFNAME != x ]; then

        # Do some preliminary tests on the input dataset definition.
        # If dataset definition returns zero files at this point, abort the job.
        # If dataset definition returns too many files compared to --nfile, create
        # a new dataset definition by adding a "with limit" clause.

        nf=`ifdh translateConstraints "defname: $SAM_DEFNAME" | wc -l`
        if [ $nf -eq 0 ]; then
          echo "Input dataset $SAM_DEFNAME is empty."
          exit 1
        fi
        if [ $NFILE -ne 0 -a $nf -gt $NFILE ]; then 
          limitdef=${SAM_PROJECT}_limit_$NFILE

          # Check whether limit def already exists.
          # Have to parse commd output because ifdh returns wrong status.

          existdef=`ifdh describeDefinition $limitdef 2>/dev/null | grep 'Definition Name:' | wc -l`
          if [ $existdef -gt 0 ]; then
            echo "Using already created limited dataset definition ${limitdef}."
          else
            ifdh createDefinition $limitdef "defname: $SAM_DEFNAME with limit $NFILE" $SAM_USER $SAM_GROUP

            # Assume command worked, because it returns the wrong status.

            echo "Created limited dataset definition ${limitdef}."
          fi

          # If we get to here, we know that we want to user $limitdef instead of $SAM_DEFNAME
          # as the input sam dataset definition.

          SAM_DEFNAME=$limitdef
        fi

        # If recursive flag, take snapshot of input dataset.

          if [ $RECUR -ne 0 ]; then
            echo "Forcing snapshot"
            SAM_DEFNAME=${SAM_DEFNAME}:force
          fi

        # Start the project.

        echo "Starting project $SAM_PROJECT using sam dataset definition $SAM_DEFNAME"
        ifdh startProject $SAM_PROJECT $SAM_STATION $SAM_DEFNAME $SAM_USER $SAM_GROUP
        if [ $? -eq 0 ]; then
          echo "Start project succeeded."
        else
          echo "Start projet failed."
          exit 1
        fi
      fi

      if [ x$SAM_DEFNAME = x ]; then

        echo "Start project requested, but no definition was specified."
        exit 1
      fi

    fi


    # Get the project url of a running project (maybe the one we just started,
    # or maybe started externally).  This command has to succeed, or we can't
    # continue.

    PURL=`ifdh findProject $SAM_PROJECT $SAM_STATION`
    if [ x$PURL = x ]; then
      echo "Unable to find url for project ${SAM_PROJECT}."
      exit 1
    else
      echo "Project url: $PURL"
    fi

    # Start the consumer process.  This command also has to succeed.

    NODE=`hostname`
    APPFAMILY=art

    # Parse fcl file to extract process_name, and use that
    # as the application name for starting the consumer process.

    APPNAME=`fhicl-dump $FCL | grep process_name: | head -1 | tr -d '"' | awk '{print $2}'`
    if [ $? -ne 0 ]; then
      echo "fhicl-dump $FCL failed to run. May be missing a ups product, library, or fcl file."
      exit 1
    fi
    if [ x$APPNAME = x ]; then
      echo "Trouble determining application name."
      echo "cat $FCL"
      cat $FCL
      exit 1
    fi

    # Make sure release version is not empty, or ifdh command line will be messed up.

    if [ x$REL = x ]; then
      REL=1
    fi

    # Make description, which is conventionally the jobsub job id.
    # This can not be empty.

    DESC=$JOBSUBJOBID
    if [ x$DESC = x ]; then
      DESC=$FCL
    fi

    echo "Starting consumer process."
    echo "ifdh establishProcess $PURL $APPNAME $REL $NODE $SAM_USER $APPFAMILY $DESC $NFILE $SAM_SCHEMA"
    CPID=`ifdh establishProcess $PURL $APPNAME $REL $NODE $SAM_USER $APPFAMILY $DESC $NFILE $SAM_SCHEMA`
    if [ x$CPID = x ]; then
      echo "Unable to start consumer process for project url ${PURL}."
      exit 1
    else
      echo "Consumer process id $CPID"
    fi

    # Stash away the project name and consumer process id in case we need them
    # later for bookkeeping.

    echo $SAM_PROJECT > sam_project.txt
    echo $CPID > cpid.txt

  fi
 
  # Sam stuff for secondary input.

  if [ $MIX_SAM -ne 0 ]; then
    echo "In Mix SAM if" 

    # Make sure a project name has been specified.

    if [ x$MIX_PROJECT = x ]; then
      echo "No mix sam project was specified."
      exit 1
    fi
    echo "Mix project: $MIX_PROJECT"

    # Start mix project (if requested).

    if [ $SAM_START -ne 0 ]; then
      if [ x$MIX_DEFNAME != x ]; then

        echo "Starting project $MIX_PROJECT using sam dataset definition $MIX_DEFNAME"
        ifdh startProject $MIX_PROJECT $SAM_STATION $MIX_DEFNAME $SAM_USER $SAM_GROUP
        if [ $? -eq 0 ]; then
          echo "Start project succeeded."
        else
          echo "Start projet failed."
          exit 1
        fi
      fi

      if [ x$MIX_DEFNAME = x ]; then

        echo "Start project requested, but no mix definition was specified."
        exit 1
      fi
    fi
  fi

  #Figure out output file names.
  #If outfile is not defined and we are inputing a single file or file list, follow our 
  #convention that the output file should be %inputfilename_%systemtime_stage.root

  # Construct options for lar command line.

  LAROPT="-c $FCL --rethrow-default"
  echo "Laropt: $LAROPT"
  if [ -f condor_lar_input.list -a $stage -eq 0 ]; then
    if [ "$INMODE" != 'textfile' ]; then
      LAROPT="$LAROPT -S condor_lar_input.list" #artroot files to read in
      #AOUTFILE=`cat condor_lar_input.list`
    fi
  fi
 
  # Extract output file name for this stage.

  if echo $OUTFILE | grep -q :; then
    outfile=''
  else
    outfile=$OUTFILE
  fi
  field=$(( $stage + 1 ))
  outfile_stage=`echo $OUTFILE | cut -d: -f$field`
  if [ x$outfile_stage != x ]; then
    outfile=$outfile_stage
  fi
  if [ x$outfile != x ]; then
    LAROPT="$LAROPT -o `basename $outfile .root`$stage.root"
    outstem=`basename $OUTFILE .root` 
  fi

  if [ x$TFILE != x ]; then
    LAROPT="$LAROPT -T $TFILE"
  fi

  if [ $NEVT -ne 0 ]; then
    LAROPT="$LAROPT -n $NEVT"  
  fi

  if [ $NSKIP -ne 0 ]; then
    LAROPT="$LAROPT --nskip $NSKIP"
  fi

  if [ x$PURL != x -a $stage -eq 0 ]; then
    LAROPT="$LAROPT --sam-web-uri $PURL"
  fi

  if [ x$CPID != x -a $stage -eq 0 ]; then
    LAROPT="$LAROPT --sam-process-id $CPID"
  fi

  if [ -n "$ARGS" ]; then
    LAROPT="$LAROPT $ARGS"  
  fi
 
  # Source optional midstage initialization scripts.

  if [ x$MIDSOURCE != x ]; then
    echo "Sourcing midstage initialization source script ${MIDSOURCE}."
    . $MIDSOURCE
    status=$?
    if [ $status -ne 0 ]; then
      exit $status
    fi
  fi

  if [ $stage -ne 0 ]; then
    LAROPT="$LAROPT -s $next_stage_input"
  fi 

  # Save a copy of the environment, which can be helpful for debugging.

  env > env${stage}.txt

  # Save a canonicalized version of the fcl configuration.

  fhicl-dump $FCL > cfgStage$stage.fcl

  # Dump proxy information.

  echo
  echo "Proxy:"
  echo
  voms-proxy-info -all

  # Run lar.
  pwd

  # Extract this stage exe.

  if echo $EXE | grep -q :; then
    exe='lar'
  else
    exe=$EXE
  fi
  field=$(( $stage + 1 ))
  exe_stage=`echo $EXE | cut -d: -f$field`
  if [ x$exe_stage != x ]; then
    exe=$exe_stage
  fi
  echo "$exe $LAROPT"
  echo "$exe $LAROPT" > commandStage$stage.txt
  $exe $LAROPT > larStage$stage.out 2> larStage$stage.err
  stat=$?
  echo $stat > larStage$stage.stat
  echo "$exe completed with exit status ${stat}."
  if [ $stat -ne 0 ]; then
    echo
    echo "Proxy:"
    echo
    voms-proxy-info -all
    echo
    echo "tail -1000 larStage$stage.out"
    echo
    tail -1000 larStage$stage.out
    echo
    echo "tail -1000 larStage$stage.err"
    echo
    tail -1000 larStage$stage.err
    echo
  fi

  # Sam cleanups.

  if [ $USE_SAM -ne 0 -a $stage -eq 0 ]; then

    # Get list of consumed files.

    if [ x$CPID = x -a -f cpid.txt ]; then
      CPID=`cat cpid.txt`
    fi
    ifdh translateConstraints "consumer_process_id $CPID and consumed_status consumed" > consumed_files.list

    # End consumer process.

    ifdh endProcess $PURL $CPID

    # Stop project (if appropriate).

    nprj=`ifdh translateConstraints "snapshot_for_project_name $SAM_PROJECT" | wc -l`
    nconsumed=`ifdh translateConstraints "project_name $SAM_PROJECT and consumed_status consumed" | wc -l`
    echo "$nprj files in project, $nconsumed files consumed so far."

    if [ $SAM_START -ne 0 -o \( $nprj -gt 0 -a $nconsumed -eq $nprj \) ]; then
      echo "Stopping project."
      ifdh endProject $PURL
    fi
  fi

  #If lar returns a status other than 0, do not move on to other stages
  if [ $stat -ne 0 ]; then
    break
  fi
 
  # Run optional midstage script.

  if [ x$MIDSCRIPT != x ]; then
    echo "Running midstage finalization script ${MIDSCRIPT}."
    ./${MIDSCRIPT} $stage
    status=$?
    if [ $status -ne 0 ]; then
      exit $status
    fi
  fi

  # Delete temporary input file.

  if [ $stage -ne 0 ]; then
   rm -rf $next_stage_input
  fi
 
  #echo `ls -t1 *.root | egrep -v 'hist|larlite|larcv' | head -n1`
 
  #echo "Outfile is $OUTFILE"
   

  next_stage_input=`ls -t1 *.root | egrep -v 'celltree|hist|larlite|larcv|Supplemental|TGraphs' | head -n1`

  # Don't let file name get too long.

  nc=`echo $next_stage_input | wc -c`
  if [ $nc -ge 200 ]; then
    base=`basename $next_stage_input`
    ext=${base##*.}
    stem=${base%.*}
    newstem=`echo $stem | cut -c1-150`_`uuidgen`
    echo "mv $next_stage_input ${newstem}.${ext}"
    mv $next_stage_input ${newstem}.${ext}
    next_stage_input=${newstem}.${ext}
  fi

  mixed_files=`sam_metadata_dumper $next_stage_input | grep mixparent | awk -F ":" '{gsub("\"" ,""); gsub(",",""); gsub(" ",""); print $2}' | sort -u`
 
  if [ x"$mixed_files" != x ]; then
    aunt_files=("${aunt_files[@]}" $mixed_files)
  fi

  stage=$[$stage +1]
 
  #rename the mem and time profile DBs by stage
  
  if [ -f time.db ]; then
    mv time.db time$stage.db
  fi
  if [ -f mem.db ]; then
    mv mem.db mem$stage.db
  fi

done

# Done looping over stages.

# Secondary sam cleanups.

if [ $MIX_SAM -ne 0 ]; then

  # Stop project (if appropriate).

  if [ $SAM_START -ne 0 ]; then
    echo "Stopping project."
    MURL=`ifdh findProject $MIX_PROJECT $SAM_STATION`
    ifdh endProject $MURL
  fi
fi

# Delete input files.

if [ $USE_SAM -eq 0 -a x$SAM_SCHEMA != xroot -a -f condor_lar_input.list ]; then
  while read file; do
    rm -f $file
  done < condor_lar_input.list
fi

# Run optional end-of-job script.

if [ x$ENDSCRIPT != x ]; then
  echo "Running end-of-job script ${ENDSCRIPT}."
  ./${ENDSCRIPT}
  status=$?
  if [ $status -ne 0 ]; then
    exit $status
  fi
fi

# Do root file checks.

# Randomize names of data files that have a corresponding json file.
# These are normally histogram files.  Art files do not have external
# json metadata at this point.

# Also randomize the names of data files if there is no input specified
# for this job (i.e. generator jobs).

# Also randomize and shorten names of data files that are longer than
# 200 characters.

# Also randomize data files that are already declared to sam.

ran=0
if [ $USE_SAM -eq 0 -a x$INFILE = x -a x$INLIST = x ]; then
  ran=1
fi

for ftype in ${DATAFILETYPES[*]}; do
  for datafile in *.${ftype}; do
    if [ -f $datafile ]; then
      nc=`echo $datafile | wc -c`
      if ifdh getMetadata $datafile > /dev/null 2> /dev/null; then
        nc=200
      fi
      if [ -f ${datafile}.json -o $ran != 0 -o $nc -ge 200 ]; then
        base=`basename $datafile`
        ext=${base##*.}
        stem=${base%.*}
        newstem=`echo $stem | cut -c1-150`_`uuidgen`
        echo "mv $datafile ${newstem}.${ext}"
        mv $datafile ${newstem}.${ext}
        if [ -f ${datafile}.json ]; then
          mv ${datafile}.json ${newstem}.${ext}.json
        fi
      fi
    fi
  done
done

# Calculate root metadata for all data files and save as json file.
# If json metadata already exists, merge with newly geneated root metadata.

for ftype in ${DATAFILETYPES[*]}; do
  for datafile in *.${ftype}; do
    if [ -f $datafile ]; then
      json=${datafile}.json
      if [ -f $json ]; then
        ./root_metadata.py --output="${json}2" "$datafile" >& /dev/null
        ./merge_json.py $json ${json}2 > ${json}3
        mv -f ${json}3 $json
        rm ${json}2
      else
        ./root_metadata.py --output="$json" "$datafile" >& /dev/null
      fi
    fi
  done
done

#create a master lar.stat file which contains the overall exit code of all stages
stageStat=0
overallStat=0
while [ $stageStat -lt $nfcls ]; do
  stat=`cat larStage$stageStat.stat`
  if [[ "$stat" = 65 && $ART_VERSION < v2_01 ]]; then
   # Workaround TimeTracker crash bug for input files with zero events. 
    for json in *.json; do  
        if grep -q '"events": *"0"' $json; then
         stat=0
        fi
    done
  fi    
  overallStat=$[$stat+$overallStat]
  
  #do some cleanup of intermediate files
  #rm Stage$stageStat.fcl  
  stageStat=$[$stageStat +1] 
done
echo $overallStat > lar.stat
valstat=$overallStat

# Make local output directories for files that we have to save.

mkdir out
mkdir log

# Stash all of the files we want to save in the local directories that we just created.

# First move data files and corresponding .json files into the out and log subdirectories.

for ftype in ${DATAFILETYPES[*]}; do
  for datafile in *.${ftype}; do
    if [ -f $datafile ]; then
      mv $datafile out
      if [ -f ${datafile}.json ]; then
        mv ${datafile}.json log
      fi
    fi
  done
done

# Move any remaining files into the log subdirectory.

for outfile in *; do
  if [ -f $outfile ]; then
    mv $outfile log
  fi
done

# Do validation (if requested).

if [ $VALIDATE_IN_JOB -eq 1 ]; then
    #If SAM was used, get the parent files based on the cpid
    if [ $USE_SAM -ne 0 ]; then
      id=`cat log/cpid.txt`
      parent_files=($(ifdh translateConstraints "consumer_process_id=$id and consumed_status consumed"))
      stat=$?
      if [ $stat -ne 0 ]; then
        echo "Failed to determine parentage."
        #exit 1
      fi
    fi
    
    echo "The file's parents are: "
    
    for elt in ${parent_files[*]};
    do
      echo $elt
    done 
    
    echo "The file's aunts are: "
    for elt in ${aunt_files[*]};
    do
      echo $elt
    done  
    
    #if we are maintain the output's parentage, combine the file's parents and aunts into a flat string
    #this string will be interpretted by validate_in_job.py. If these are left empty, then validate_in_job will not change the file's parentage
    if [ $MAINTAIN_PARENTAGE -eq 1 ]; then
       export JOBS_PARENTS=`echo ${parent_files[*]}`
       export JOBS_AUNTS=`echo ${aunt_files[*]}`
    fi
    
    # Do validation function for the whole job.

    valstat=$overallStat
    if [ $valstat -eq 0 ]; then
      curdir=`pwd`
      cd $curdir/log
      dataopt=''
      for ftype in ${DATAFILETYPES[*]}; do
        dataopt="$dataopt --data_file_type $ftype"
      done
      echo "./validate_in_job.py --dir $curdir/out --logfiledir $curdir/log --outdir $OUTDIR/$OUTPUT_SUBDIR --declare $DECLARE_IN_JOB --copy $COPY_TO_FTS --maintain_parentage $MAINTAIN_PARENTAGE $dataopt"
      ./validate_in_job.py --dir $curdir/out --logfiledir $curdir/log --outdir $OUTDIR/$OUTPUT_SUBDIR --declare $DECLARE_IN_JOB --copy $COPY_TO_FTS --maintain_parentage $MAINTAIN_PARENTAGE $dataopt
      valstat=$?
      cd $curdir
    fi

fi

# Make a tarball of the log directory contents, and save the tarball in the log directory.

rm -f log.tar
tar -cjf log.tar -C log .
mv log.tar log

# For copy back, setup up current version of ifdhc.
# May be different than version setup by larsoft.

echo "Setting up current version of ifdhc."
if [ x$IFDHC_DIR != x ]; then
  unsetup ifdhc
fi
setup ifdhc
echo "IFDHC_DIR=$IFDHC_DIR"

# Create remote output and log directories.

export IFDH_CP_MAXRETRIES=5

echo "Make directory ${LOGDIR}/${OUTPUT_SUBDIR}."
date
subdir=$OUTPUT_SUBDIR
dir=$LOGDIR
while echo $subdir | grep -q /; do
  dir=${dir}/${subdir%%/*}
  subdir=${subdir#*/}
  echo "ifdh mkdir $IFDH_OPT $dir"
  ifdh mkdir $IFDH_OPT $dir
done
echo "ifdh mkdir $IFDH_OPT ${LOGDIR}/$OUTPUT_SUBDIR"
ifdh mkdir $IFDH_OPT ${LOGDIR}/$OUTPUT_SUBDIR
echo "Done making directory ${LOGDIR}/${OUTPUT_SUBDIR}."
date

if [ ${OUTDIR} != ${LOGDIR} ]; then
  echo "Make directory ${OUTDIR}/${OUTPUT_SUBDIR}."
  date
  subdir=$OUTPUT_SUBDIR
  dir=$OUTDIR
  while echo $subdir | grep -q /; do
    dir=${dir}/${subdir%%/*}
    subdir=${subdir#*/}
    echo "ifdh mkdir $IFDH_OPT $dir"
    ifdh mkdir $IFDH_OPT $dir
  done
  echo "ifdh mkdir $IFDH_OPT ${OUTDIR}/$OUTPUT_SUBDIR"
  ifdh mkdir $IFDH_OPT ${OUTDIR}/$OUTPUT_SUBDIR
  echo "Done making directory ${OUTDIR}/${OUTPUT_SUBDIR}."
  date
fi

# Transfer tarball in log subdirectory.

statout=0
echo "ls log"
ls log
echo "ifdh cp -D $IFDH_OPT log/log.tar ${LOGDIR}/$OUTPUT_SUBDIR"
ifdh cp -D $IFDH_OPT log/log.tar ${LOGDIR}/$OUTPUT_SUBDIR
date
stat=$?
if [ $stat -ne 0 ]; then
  statout=1
  echo "ifdh cp failed with status ${stat}."
fi

# Transfer data files in out subdirectory.

if [ $COPY_TO_FTS -eq 0 ]; then

  if [ "$( ls -A out )" ]; then
    echo "ifdh cp -D $IFDH_OPT out/* ${OUTDIR}/$OUTPUT_SUBDIR"
    ifdh cp -D $IFDH_OPT out/* ${OUTDIR}/$OUTPUT_SUBDIR
    stat=$?
    if [ $stat -ne 0 ]; then
      statout=1
      echo "ifdh cp failed with status ${stat}."
    fi
  fi

fi  

if [ $statout -eq 0 -a -f log/lar.stat ]; then
  statout=`cat log/lar.stat`
fi

if [ $statout -eq 0 ]; then
  statout=$valstat
fi  

exit $statout