#!/bin/sh -f
# set -x
#
#  Based on globus submission script for pbs
#
#  Submits job to PBS.
#  Input: path to grami file (same as Globus).
#
# The temporary job script is created for the submission and then removed 
# at the end of this script. 


echo "----- starting submit_pbs_job -----" 1>&2
joboption_lrms=PBS
walltime_ratio='11/10'
##############################################################
# These should be set automatically
##############################################################
# Path to pbs commands
PBS_BIN_PATH=${PBS_BIN_PATH:-/usr/bin}
# Where to store temporary files on gatekeeper
TMP_DIR=${TMP_DIR:-/tmp}
# Where runtime scripts can be found on computing nodes (empty if does not exist)
RUNTIME_CONFIG_DIR=${RUNTIME_CONFIG_DIR:-}
# Where GNU time utility is located on computing nodes (empty if does not exist)
GNU_TIME=${GNU_TIME:-/usr/bin/time}
# Command to get name of executing node
NODENAME=${NODENAME:-/bin/hostname -f}
# Description of (cross-)mounted disc space on cluster
RUNTIME_LOCAL_SCRATCH_DIR=${RUNTIME_LOCAL_SCRATCH_DIR:-}
RUNTIME_FRONTEND_SEES_NODE=${RUNTIME_FRONTEND_SEES_NODE:-}
RUNTIME_NODE_SEES_FRONTEND=${RUNTIME_NODE_SEES_FRONTEND:-}
RUNTIME_NORDUGRID_LOCATION="$NORDUGRID_LOCATION"
RUNTIME_GLOBUS_LOCATION="$GLOBUS_LOCATION"

#default is NFS
if [ -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
  RUNTIME_NODE_SEES_FRONTEND=yes
fi
# locally empty means no
if [ "${RUNTIME_NODE_SEES_FRONTEND}" = 'no' ] ; then
  RUNTIME_NODE_SEES_FRONTEND=
fi



arg_file=$1
##############################################################
# Source the argument file. 
##############################################################
if [ -z "$arg_file" ] ; then
   echo "Arguments file should be specified" 1>&2
   exit 1
fi
if [ ! -f $arg_file ] ; then
   echo "Missing arguments file" 1>&2
   exit 1
fi
. $arg_file

if [ -z "$joboption_controldir" ] ; then
  joboption_controldir=`dirname "$arg_file"`
  if [ "$joboption_controldir" = '.' ] ; then
    joboption_controldir="$PWD"
  fi
fi
if [ -z "$joboption_gridid" ] ; then
  joboption_gridid=`basename "$arg_file" | sed 's/^job\.\(.*\)\.grami$/\1/'`
fi

if [ -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
  if [ -z "${RUNTIME_LOCAL_SCRATCH_DIR}" ] ; then
    echo "Need to know at which directory to run job: RUNTIME_LOCAL_SCRATCH_DIR must be set if RUNTIME_NODE_SEES_FRONTEND is empty" 1>&2
    exit 1
  fi
fi

##############################################################
# combine arguments to command -  easier to use
##############################################################
i=0
joboption_args=
eval "var_is_set=\${joboption_arg_$i+yes}"
while [ ! -z "${var_is_set}" ] ; do
  eval "var_value=\${joboption_arg_$i}"
  joboption_args="$joboption_args \"${var_value}\""
  i=$(( i + 1 ))
  eval "var_is_set=\${joboption_arg_$i+yes}"
done

##############################################################
# Zero stage of runtime environments
##############################################################
joboption_num=0
eval "var_is_set=\${joboption_runtime_$joboption_num+yes}"
while [ ! -z "${var_is_set}" ] ; do
  eval "var_value=\${joboption_runtime_$joboption_num}"
  if [ -r "$RUNTIME_CONFIG_DIR/${var_value}" ] ; then
    . "$RUNTIME_CONFIG_DIR/${var_value}" "0"
  else
    echo "Warning: runtime script ${var_value} is missing" 1>&2
  fi
  joboption_num=$(( joboption_num + 1 ))
  eval "var_is_set=\${joboption_runtime_$joboption_num+yes}"
done

PBS_QSUB='qsub -r n -S /bin/sh -m n '
if [ ! -z "$PBS_BIN_PATH" ] ; then
  PBS_QSUB=${PBS_BIN_PATH}/${PBS_QSUB}
fi

tmpdir=${TMP_DIR:-/tmp}

# File name to be used for temporary job script
PBS_JOB_SCRIPT=`mktemp ${tmpdir}/pbs_job_script.XXXXXX`
if [ -z "$PBS_JOB_SCRIPT" ] ; then 
  echo "Creation of temporary file failed"
  exit 1
fi
PBS_JOB_OUT="${PBS_JOB_SCRIPT}.out"
touch $PBS_JOB_OUT
PBS_JOB_ERR="${PBS_JOB_SCRIPT}.err"
touch $PBS_JOB_ERR
if [ ! -f "$PBS_JOB_SCRIPT" ] || [ ! -f "$PBS_JOB_OUT" ] || [ ! -f "$PBS_JOB_ERR" ] ; then 
  echo "Something is wrong. Either somebody is playing bad or can't write to ${tmpdir}"
  exit 1
fi

is_cluster=true

##############################################################
# Start job script
##############################################################
echo "# PBS batch job script built by grid-manager" > $PBS_JOB_SCRIPT
# write PBS output to 'comment' file
echo "#PBS -e '${joboption_directory}.comment'">> $PBS_JOB_SCRIPT
echo "#PBS -j eo">> $PBS_JOB_SCRIPT
echo "" >> $PBS_JOB_SCRIPT
# choose queue
if [ ! -z "${joboption_queue}" ] ; then
  echo "#PBS -q $joboption_queue" >> $PBS_JOB_SCRIPT
fi
# project name for accounting
if [ ! -z "${joboption_project}" ] ; then
  echo "#PBS -A $joboption_project" >> $PBS_JOB_SCRIPT
fi
# job name for convenience
if [ ! -z "${joboption_jobname}" ] ; then
  jobname=`echo "$joboption_jobname" | \
           sed 's/^\([^[:alpha:]]\)/N\1/' | \
           sed 's/[^[:alnum:]]/_/g' | \
	   sed 's/\(...............\).*/\1/'`
  echo "#PBS -N '$jobname'" >> $PBS_JOB_SCRIPT
fi
echo "PBS jobname: $jobname" 1>&2

##############################################################
# (non-)parallel jobs
##############################################################
if [ -z "$joboption_count" ] ; then 
  joboption_count=1
elif [ "$joboption_count" -le 0 ] ; then
  joboption_count=1
fi

nodes_string="#PBS -l nodes=${joboption_count}"
i=0
eval "var_is_set=\${joboption_nodeproperty_$i+yes}"
while [ ! -z "${var_is_set}" ] ; do
  eval "var_value=\${joboption_nodeproperty_$i}"
  nodes_string="${nodes_string}:${var_value}"
  i=$(( i + 1 ))
  eval "var_is_set=\${joboption_nodeproperty_$i+yes}"
done
echo "$nodes_string" >> $PBS_JOB_SCRIPT

##############################################################
# Execution times (minutes)
##############################################################
if [ ! -z "$joboption_cputime" ] ; then
# TODO: parallel jobs, add initialization time, make walltime bigger, ...
# is cputime for every process ?
  if [ $joboption_cputime -lt 0 ] ; then
    joboption_cputime=0
  fi
  maxwalltime=$(( $joboption_cputime * $walltime_ratio ))
#  echo "#PBS -l pcput=$joboption_cputime:00" >> $PBS_JOB_SCRIPT
  echo "#PBS -l cput=$joboption_cputime:00" >> $PBS_JOB_SCRIPT
  echo "#PBS -l walltime=$maxwalltime:00" >> $PBS_JOB_SCRIPT
fi

##############################################################
# Requested memory (mb)
##############################################################
if [ "$joboption_localtransfer" = 'yes' ] ; then
  # downloader and uploader can take a lot of memory
  if [ -z "$joboption_memory" ] ; then
    joboption_memory=1000
  else
    if [ "$joboption_memory" -lt 1000 ] ; then
      joboption_memory=1000
    fi
  fi
fi
if [ ! -z "$joboption_memory" ] ; then
  echo "#PBS -l pvmem=${joboption_memory}mb" >> $PBS_JOB_SCRIPT
  echo "#PBS -l vmem=${joboption_memory}mb" >> $PBS_JOB_SCRIPT
  echo "#PBS -l mem=${joboption_memory}mb" >> $PBS_JOB_SCRIPT
fi

# Start time 
#if [ "${joboption_starttime}" -ne 0 ] ; then
#  start_time=$joboption_starttime
#  # This has to be MDS style time. Convert to PBS style
#  start_time=`echo "$start_time" | \
#              sed 's/\([^Z]*\).*/\1/' | \
#	      sed 's/\(.*\)\(..\)$/\1.\2/'`
#  echo "#PBS -a ${start_time}" >> $PBS_JOB_SCRIPT    
#fi


gate_host=`uname -n`
if [ -z "$gate_host" ] ; then 
  echo "Can't get own hostname" 1>&2
  rm -f "$PBS_JOB_SCRIPT" "$PBS_JOB_OUT" "$PBS_JOB_ERR"
  exit 1
fi

##############################################################
#  PBS stage in/out
##############################################################
if [ -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
  (
    cd "$joboption_directory"
    if [ $? -ne '0' ] ; then 
      echo "Can't change to session directory: $joboption_directory" 1>&2
      exit 1
    fi
    scratch_dir=`dirname "$joboption_directory"`
    echo "#PBS -W stagein=$RUNTIME_LOCAL_SCRATCH_DIR@$gate_host:$joboption_directory" >> $PBS_JOB_SCRIPT
    echo "#PBS -W stageout=$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid@$gate_host:$scratch_dir" >> $PBS_JOB_SCRIPT
    echo "#PBS -W stageout=$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid.diag@$gate_host:$joboption_directory.diag" >> $PBS_JOB_SCRIPT
  )
fi

echo "" >> $PBS_JOB_SCRIPT
echo "# Overide umask of execution node (sometime values are really strange)" >> $PBS_JOB_SCRIPT
echo "umask 077" >> $PBS_JOB_SCRIPT

##############################################################
# Add environment variables
##############################################################
echo "# Setting environment variables as specified by user" >> $PBS_JOB_SCRIPT
i=0
eval "var_is_set=\${joboption_env_$i+yes}"
while [ ! -z "${var_is_set}" ] ; do
  eval "var_value=\${joboption_env_$i}"
  echo "export ${var_value}" >> $PBS_JOB_SCRIPT
  i=$(( i + 1 ))
  eval "var_is_set=\${joboption_env_$i+yes}"
done
echo "" >> $PBS_JOB_SCRIPT


##############################################################
# Check for existance of executable,
# there is no sense to check for executable if files are 
# downloaded directly to computing node
##############################################################
if [ -z "${joboption_arg_0}" ] ; then
  echo 'Executable is not specified' 1>&2
  exit 1
fi
if [ ! "$joboption_localtransfer" = 'yes' ] ; then
  program_start=`echo ${joboption_arg_0} | head -c 1 2>&1`
  if [ "$program_start" != '$' ] && [ "$program_start" != '/' ] ; then
    if [ ! -f $joboption_directory/${joboption_arg_0} ] ; then 
      echo 'Executable does not exist' 1>&2
      exit 1
    fi
    if [ ! -x $joboption_directory/${joboption_arg_0} ] ; then 
      echo 'Executable is not executable' 1>&2
      exit 1
    fi
  fi
fi
#######################################################################
# copy information useful for transfering files to/from node directly
#######################################################################
if [ "$joboption_localtransfer" = 'yes' ] ; then
  RUNTIME_CONTROL_DIR=`mktemp ${joboption_directory}/control.XXXXXX`
  if [ -z "$RUNTIME_CONTROL_DIR" ] ; then
    echo 'Failed to choose name for temporary control directory' 1>&2
    exit 1
  fi
  rm -f "$RUNTIME_CONTROL_DIR"
  mkdir "$RUNTIME_CONTROL_DIR"
  if [ $? -ne '0' ] ; then
    echo 'Failed to create temporary control directory' 1>&2
    exit 1
  fi
  chmod go-rwx,u+rwx "${RUNTIME_CONTROL_DIR}"
  echo '' >"${RUNTIME_CONTROL_DIR}/job.local.proxy"
  chmod go-rw,u+r,a-x "${RUNTIME_CONTROL_DIR}/job.local.proxy"
  cat "${joboption_controldir}/job.${joboption_gridid}.proxy" >"${RUNTIME_CONTROL_DIR}/job.local.proxy"
  cat "${joboption_controldir}/job.${joboption_gridid}.input" >"${RUNTIME_CONTROL_DIR}/job.local.input"
  cat "${joboption_controldir}/job.${joboption_gridid}.output" >"${RUNTIME_CONTROL_DIR}/job.local.output"
  RUNTIME_CONTROL_DIR_REL=`basename "$RUNTIME_CONTROL_DIR"`
  echo "$RUNTIME_CONTROL_DIR_REL *.*" >>"${RUNTIME_CONTROL_DIR}/job.local.input"
  echo "$RUNTIME_CONTROL_DIR_REL" >>"${RUNTIME_CONTROL_DIR}/job.local.output"
  echo "$RUNTIME_CONTROL_DIR_REL" >>"${joboption_controldir}/job.${joboption_gridid}.output"
  RUNTIME_STDOUT_REL=`echo "${joboption_stdout}" | sed "s#^${joboption_directory}##"`
  RUNTIME_STDERR_REL=`echo "${joboption_stderr}" | sed "s#^${joboption_directory}##"`
  echo "$RUNTIME_STDOUT_REL *.*" >>"${RUNTIME_CONTROL_DIR}/job.local.input"
  echo "$RUNTIME_STDERR_REL *.*" >>"${RUNTIME_CONTROL_DIR}/job.local.input"
  echo "RUNTIME_CONTROL_DIR=$RUNTIME_CONTROL_DIR" >> $PBS_JOB_SCRIPT
fi

######################################################################
# Adjust working directory for tweaky nodes
# RUNTIME_GRIDAREA_DIR should be defined by external means on nodes
######################################################################
if [ ! -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
  echo "RUNTIME_JOB_DIR=$joboption_directory" >> $PBS_JOB_SCRIPT
  echo "RUNTIME_JOB_DIAG=${joboption_directory}.diag" >> $PBS_JOB_SCRIPT
  echo "RUNTIME_JOB_STDIN=$joboption_stdin" >> $PBS_JOB_SCRIPT
  echo "RUNTIME_JOB_STDOUT=$joboption_stdout" >> $PBS_JOB_SCRIPT
  echo "RUNTIME_JOB_STDERR=$joboption_stderr" >> $PBS_JOB_SCRIPT
  echo "if [ ! -z \"\$RUNTIME_GRIDAREA_DIR\" ] ; then" >> $PBS_JOB_SCRIPT
  echo "  RUNTIME_JOB_DIR=\$RUNTIME_GRIDAREA_DIR/\`basename \$RUNTIME_JOB_DIR\`" >> $PBS_JOB_SCRIPT
  echo "  RUNTIME_JOB_STDIN=\`echo \"\$RUNTIME_JOB_STDIN\" | sed \"s#^$joboption_directory#\$RUNTIME_JOB_DIR#\"\`" >> $PBS_JOB_SCRIPT
  echo "  RUNTIME_JOB_STDOUT=\`echo \"\$RUNTIME_JOB_STDOUT\" | sed \"s#^$joboption_directory#\$RUNTIME_JOB_DIR#\"\`" >> $PBS_JOB_SCRIPT
  echo "  RUNTIME_JOB_STDERR=\`echo \"\$RUNTIME_JOB_STDERR\" | sed \"s#^$joboption_directory#\$RUNTIME_JOB_DIR#\"\`" >> $PBS_JOB_SCRIPT
  echo "  RUNTIME_JOB_DIAG=\`echo \"\$RUNTIME_JOB_DIAG\" | sed \"s#^$joboption_directory#\$RUNTIME_JOB_DIR#\"\`" >> $PBS_JOB_SCRIPT
  echo "  RUNTIME_CONTROL_DIR=\`echo \"\$RUNTIME_CONTROL_DIR\" | sed \"s#^$joboption_directory#\$RUNTIME_JOB_DIR#\"\`" >> $PBS_JOB_SCRIPT
  echo "fi" >> $PBS_JOB_SCRIPT
else
  echo "RUNTIME_JOB_DIR=$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid" >> $PBS_JOB_SCRIPT
  echo "RUNTIME_JOB_DIAG=$RUNTIME_LOCAL_SCRATCH_DIR/${joboption_gridid}.diag" >> $PBS_JOB_SCRIPT
  echo "RUNTIME_GRIDAREA_DIR=" >> $PBS_JOB_SCRIPT
  RUNTIME_STDIN_REL=`echo "${joboption_stdin}" | sed "s#^${joboption_directory}/*##"`
  RUNTIME_STDOUT_REL=`echo "${joboption_stdout}" | sed 's#^${joboption_directory}/*##'`
  RUNTIME_STDERR_REL=`echo "${joboption_stderr}" | sed 's#^${joboption_directory}/*##'`
  if [ "$RUNTIME_STDIN_REL" = "${joboption_stdin}" ] ; then
    echo "RUNTIME_JOB_STDIN=\"${joboption_stdin}\"" >> $PBS_JOB_SCRIPT
  else
    echo "RUNTIME_JOB_STDIN=\"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$RUNTIME_STDIN_REL\"" >> $PBS_JOB_SCRIPT
  fi

  if [ "$RUNTIME_STDOUT_REL" = "${joboption_stdout}" ] ; then
    echo "RUNTIME_JOB_STDOUT=\"${joboption_stdout}\"" >> $PBS_JOB_SCRIPT
  else
    echo "RUNTIME_JOB_STDOUT=\"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$RUNTIME_STDOUT_REL\"" >> $PBS_JOB_SCRIPT
  fi
  if [ "$RUNTIME_STDERR_REL" = "${joboption_stderr}" ] ; then
    echo "RUNTIME_JOB_STDERR=\"${joboption_stderr}\"" >> $PBS_JOB_SCRIPT
  else
    echo "RUNTIME_JOB_STDERR=\"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$RUNTIME_STDERR_REL\"" >> $PBS_JOB_SCRIPT
  fi
fi

##############################################################
# Add std... to job arguments
##############################################################
if [ ! -z "$joboption_stdin" ] ; then
  joboption_args="$joboption_args <\$RUNTIME_JOB_STDIN"
fi
if [ ! -z "$joboption_stdout" ] ; then
  joboption_args="$joboption_args 1>\$RUNTIME_JOB_STDOUT"
fi
if [ ! -z "$joboption_stderr" ] ; then
  if [ X"$joboption_stderr" = X"$joboption_stdout" ] ; then
    joboption_args="$joboption_args 2>&1"
  else
    joboption_args="$joboption_args 2>\$RUNTIME_JOB_STDERR"
  fi
fi

##############################################################
#  Move files to local working directory (job is done on node only)
#  RUNTIME_JOB_DIR -> RUNTIME_LOCAL_SCRATCH_DIR/job_id
##############################################################
echo "RUNTIME_LOCAL_SCRATCH_DIR=\${RUNTIME_LOCAL_SCRATCH_DIR:-$RUNTIME_LOCAL_SCRATCH_DIR}" >> $PBS_JOB_SCRIPT
echo "RUNTIME_FRONTEND_SEES_NODE=\${RUNTIME_FRONTEND_SEES_NODE:-$RUNTIME_FRONTEND_SEES_NODE}" >> $PBS_JOB_SCRIPT
echo "RUNTIME_NODE_SEES_FRONTEND=\${RUNTIME_NODE_SEES_FRONTEND:-$RUNTIME_NODE_SEES_FRONTEND}" >> $PBS_JOB_SCRIPT
cat >> $PBS_JOB_SCRIPT <<'EOSCR'
if [ ! -z "$RUNTIME_LOCAL_SCRATCH_DIR" ] && [ ! -z "$RUNTIME_NODE_SEES_FRONTEND" ] ; then
  # moving (!!!!! race condition here - while there is no job directory
  # gridftp can create the one with the same name !!!!!)
  RUNTIME_NODE_JOB_DIR="$RUNTIME_LOCAL_SCRATCH_DIR"/`basename "$RUNTIME_JOB_DIR"`
  rm -rf "$RUNTIME_NODE_JOB_DIR"
  mv "$RUNTIME_JOB_DIR" "$RUNTIME_LOCAL_SCRATCH_DIR"
  if [ ! -z "$RUNTIME_FRONTEND_SEES_NODE" ] ; then
    # creating link for whole directory
    ln -s "$RUNTIME_FRONTEND_SEES_NODE"/`basename "$RUNTIME_JOB_DIR"` "$RUNTIME_JOB_DIR"
  else
    # keep stdout, stderr and control directory on frontend
    # recreate job directory
    mkdir "$RUNTIME_JOB_DIR"
    # make those files
    mkdir -p `dirname "$RUNTIME_JOB_STDOUT"`
    mkdir -p `dirname "$RUNTIME_JOB_STDERR"`
    touch "$RUNTIME_JOB_STDOUT"
    touch "$RUNTIME_JOB_STDERR"
    RUNTIME_JOB_STDOUT__=`echo "$RUNTIME_JOB_STDOUT" | sed "s#^${RUNTIME_JOB_DIR}#${RUNTIME_NODE_JOB_DIR}#"`
    RUNTIME_JOB_STDERR__=`echo "$RUNTIME_JOB_STDERR" | sed "s#^${RUNTIME_JOB_DIR}#${RUNTIME_NODE_JOB_DIR}#"`
    rm "$RUNTIME_JOB_STDOUT__" 2>/dev/null
    rm "$RUNTIME_JOB_STDERR__" 2>/dev/null
    if [ ! -z "$RUNTIME_JOB_STDOUT__" ] ; then
      ln -s "$RUNTIME_JOB_STDOUT" "$RUNTIME_JOB_STDOUT__"
    fi
    if [ "$RUNTIME_JOB_STDOUT__" != "$RUNTIME_JOB_STDERR__" ] ; then
      if [ ! -z "$RUNTIME_JOB_STDOUT__" ] ; then
        ln -s "$RUNTIME_JOB_STDERR" "$RUNTIME_JOB_STDERR__"
      fi
    fi
    if [ ! -z "$RUNTIME_CONTROL_DIR" ] ; then
      # move control directory back to frontend
      RUNTIME_CONTROL_DIR__=`echo "$RUNTIME_CONTROL_DIR" | sed "s#^${RUNTIME_JOB_DIR}#${RUNTIME_NODE_JOB_DIR}#"`
      mv "$RUNTIME_CONTROL_DIR__" "$RUNTIME_CONTROL_DIR"
    fi    
  fi
  # adjust stdin,stdout & stderr pointers
  RUNTIME_JOB_STDIN=`echo "$RUNTIME_JOB_STDIN" | sed "s#^${RUNTIME_JOB_DIR}#${RUNTIME_NODE_JOB_DIR}#"`
  RUNTIME_JOB_STDOUT=`echo "$RUNTIME_JOB_STDOUT" | sed "s#^${RUNTIME_JOB_DIR}#${RUNTIME_NODE_JOB_DIR}#"`
  RUNTIME_JOB_STDERR=`echo "$RUNTIME_JOB_STDERR" | sed "s#^${RUNTIME_JOB_DIR}#${RUNTIME_NODE_JOB_DIR}#"`
  RUNTIME_FRONTEND_JOB_DIR="$RUNTIME_JOB_DIR"
  RUNTIME_JOB_DIR="$RUNTIME_NODE_JOB_DIR"
fi
if [ -z "$RUNTIME_NODE_SEES_FRONTEND" ] ; then
  mkdir -p "$RUNTIME_JOB_DIR"
fi
EOSCR
echo "" >> $PBS_JOB_SCRIPT
echo "RESULT=0" >> $PBS_JOB_SCRIPT
echo "" >> $PBS_JOB_SCRIPT


#####################################################
#  Download input files
####################################################
if [ "$joboption_localtransfer" = 'yes' ] ; then
echo "NORDUGRID_LOCATION=\${NORDUGRID_LOCATION:-$RUNTIME_NORDUGRID_LOCATION}" >> $PBS_JOB_SCRIPT
echo "GLOBUS_LOCATION=\${GLOBUS_LOCATION:-$RUNTIME_GLOBUS_LOCATION}" >> $PBS_JOB_SCRIPT
cat >> $PBS_JOB_SCRIPT <<'EOSCR'
if [ -z "$NORDUGRID_LOCATION" ] ; then
  echo 'Variable NORDUGRID_LOCATION is not set' 1>&2
  exit 1
fi
if [ -z "$GLOBUS_LOCATION" ] ; then
  echo 'Variable GLOBUS_LOCATION is not set' 1>&2
  exit 1
fi
export GLOBUS_LOCATION
export NORDUGRID_LOCATION
export LD_LIBRARY_PATH="$GLOBUS_LOCATION/lib:$LD_LIBRARY_PATH"
export SASL_PATH="$GLOBUS_LOCATION/lib/sasl"
export X509_USER_KEY="${RUNTIME_CONTROL_DIR}/job.local.proxy"
export X509_USER_CERT="${RUNTIME_CONTROL_DIR}/job.local.proxy"
export X509_USER_PROXY="${RUNTIME_CONTROL_DIR}/job.local.proxy"
unset X509_RUN_AS_SERVER
$NORDUGRID_LOCATION/libexec/downloader -p -c 'local' "$RUNTIME_CONTROL_DIR" "$RUNTIME_JOB_DIR" 2>>${RUNTIME_CONTROL_DIR}/job.local.errors
if [ $? -ne '0' ] ; then
  echo 'ERROR: Downloader failed.' 1>&2
  RESULT=1
fi
EOSCR
fi
#####################################################
#  Go to working dir and start job
####################################################
echo "" >> $PBS_JOB_SCRIPT
echo "# Changing to session directory" >> $PBS_JOB_SCRIPT
echo "cd \$RUNTIME_JOB_DIR" >> $PBS_JOB_SCRIPT
echo "export HOME=\$RUNTIME_JOB_DIR" >> $PBS_JOB_SCRIPT

##############################################################
#  Skip execution if something already failed
##############################################################
echo "if [ \"\$RESULT\" = '0' ] ; then" >> $PBS_JOB_SCRIPT

##############################################################
#  Runtime configuration at computing node
##############################################################
echo "# Running runtime scripts" >> $PBS_JOB_SCRIPT
echo "RUNTIME_CONFIG_DIR=\${RUNTIME_CONFIG_DIR:-$RUNTIME_CONFIG_DIR}" >> $PBS_JOB_SCRIPT
i=0
eval "var_is_set=\${joboption_runtime_$i+yes}"
echo "runtimeenvironments=" >> $PBS_JOB_SCRIPT
while [ ! -z "${var_is_set}" ] ; do
  if [ "$i" = '0' ] ; then
    echo "if [ ! -z \"\$RUNTIME_CONFIG_DIR\" ] ; then" >> $PBS_JOB_SCRIPT
  fi
  eval "  var_value=\"\${joboption_runtime_$i}\""
  echo "  if [ -r \"\${RUNTIME_CONFIG_DIR}/${var_value}\" ] ; then" >> $PBS_JOB_SCRIPT
  echo "    runtimeenvironments=\"\${runtimeenvironments}${var_value};\"" >> $PBS_JOB_SCRIPT
  echo "    source \${RUNTIME_CONFIG_DIR}/${var_value} 1 " >> $PBS_JOB_SCRIPT
  echo "  fi" >> $PBS_JOB_SCRIPT
  i=$(( i + 1 ))
  eval "var_is_set=\${joboption_runtime_$i+yes}"
done
if [ ! "$i" = '0' ] ; then
  echo "fi" >> $PBS_JOB_SCRIPT
fi
echo "" >> $PBS_JOB_SCRIPT


##############################################################
#  Diagnostics
##############################################################
echo "echo \"runtimeenvironments=\$runtimeenvironments\" >> \"\$RUNTIME_JOB_DIAG\"" >> $PBS_JOB_SCRIPT
#if [ "$joboption_count" -ne '1' ] ; then
cat >> $PBS_JOB_SCRIPT <<'EOSCR'
if [ ! "X$PBS_NODEFILE" = 'X' ] ; then
  if [ -r "$PBS_NODEFILE" ] ; then
    cat "$PBS_NODEFILE" | sed 's/\(.*\)/nodename=\1/' >> "$RUNTIME_JOB_DIAG"
  else
    PBS_NODEFILE=
  fi
fi
EOSCR
#fi
if [ ! -z "$NODENAME" ] ; then
  echo 'if [ "X$PBS_NODEFILE" = X ] ; then' >> $PBS_JOB_SCRIPT
  echo "  nodename=\`$NODENAME\`" >> $PBS_JOB_SCRIPT
  echo "  echo \"nodename=\$nodename\" >> \"\$RUNTIME_JOB_DIAG\"" >> $PBS_JOB_SCRIPT
  echo 'fi' >> $PBS_JOB_SCRIPT
fi

##############################################################
#  Execution
##############################################################
if [ -z "$GNU_TIME" ] ; then 
  echo "$joboption_args" >> $PBS_JOB_SCRIPT
else
  echo "$GNU_TIME -o \"\$RUNTIME_JOB_DIAG\" -a -f '\
WallTime=%es\nKernelTime=%Ss\nUserTime=%Us\nCPUUsage=%P\n\
MaxResidentMemory=%MkB\nAverageResidentMemory=%tkB\n\
AverageTotalMemory=%KkB\nAverageUnsharedMemory=%DkB\n\
AverageUnsharedStack=%pkB\nAverageSharedMemory=%XkB\n\
PageSize=%ZB\nMajorPageFaults=%F\nMinorPageFaults=%R\n\
Swaps=%W\nForcedSwitches=%c\nWaitSwitches=%w\n\
Inputs=%I\nOutputs=%O\nSocketReceived=%r\nSocketSent=%s\n\
Signals=%k\n' \
$joboption_args" >> $PBS_JOB_SCRIPT
fi

echo "RESULT=\$?" >> $PBS_JOB_SCRIPT
echo "fi" >> $PBS_JOB_SCRIPT

##############################################################
#  Runtime (post)configuration at computing node
##############################################################
i=0
eval "var_is_set=\${joboption_runtime_$i+yes}"
while [ ! -z "${var_is_set}" ] ; do
  if [ "$i" = '0' ] ; then
    echo "if [ ! -z \"\$RUNTIME_CONFIG_DIR\" ] ; then" >> $PBS_JOB_SCRIPT
  fi
  eval "var_value=\"\${joboption_runtime_$i}\""
  echo "  if [ -r \"\${RUNTIME_CONFIG_DIR}/${var_value}\" ] ; then" >> $PBS_JOB_SCRIPT
  echo "    source \${RUNTIME_CONFIG_DIR}/${var_value} 2 " >> $PBS_JOB_SCRIPT
  echo "  fi" >> $PBS_JOB_SCRIPT
  i=$(( i + 1 ))
  eval "var_is_set=\${joboption_runtime_$i+yes}"
done
if [ ! "$i" = '0' ] ; then
  echo "fi" >> $PBS_JOB_SCRIPT
fi
echo "" >> $PBS_JOB_SCRIPT

#####################################################
#  Upload output files
####################################################
if [ "$joboption_localtransfer" = 'yes' ] ; then
cat >> $PBS_JOB_SCRIPT <<'EOSCR'
if [ "$RESULT" = '0' ] ; then
  $NORDUGRID_LOCATION/libexec/uploader -p -c 'local' "$RUNTIME_CONTROL_DIR" "$RUNTIME_JOB_DIR" 2>>${RUNTIME_CONTROL_DIR}/job.local.errors
  if [ $? -ne '0' ] ; then
    echo 'ERROR: Uploader failed.' 1>&2
    if [ "$RESULT" = '0' ] ; then RESULT=1 ; fi
  fi
fi
rm -f "${RUNTIME_CONTROL_DIR}/job.local.proxy"
EOSCR
else
# There is no sense to keep trash till GM runs uploader
  echo 'if [ ! -z  "$RUNTIME_LOCAL_SCRATCH_DIR" ] ; then' >> $PBS_JOB_SCRIPT
# Delete all files except listed in job.#.output
  echo '  find ./ -type l -exec rm -f "{}" ";"' >> $PBS_JOB_SCRIPT
  echo '  find ./ -type f -exec chmod u+w "{}" ";"' >> $PBS_JOB_SCRIPT
  if [ -f "$joboption_controldir/job.$joboption_gridid.output" ] ; then
    cat "$joboption_controldir/job.$joboption_gridid.output" | \
    sed 's/^ *"\([^"]*\)".*/\1/g;t suc;s/^ *//;s/\([^\\]\) .*/\1/;:suc;s/\\\(.\)/\1/g' | \
    { while true ; do
      read name
      if [ $? -ne '0' ] ; then break ; fi
      echo "  chmod u-w \"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$name\" 2>/dev/null" >> $PBS_JOB_SCRIPT
    done; }
  fi
  echo '  find ./ -type f -perm +200 -exec rm -f "{}" ";"' >> $PBS_JOB_SCRIPT
  echo '  find ./ -type f -exec chmod u+w "{}" ";"' >> $PBS_JOB_SCRIPT
  echo 'fi' >> $PBS_JOB_SCRIPT
fi
echo "" >> $PBS_JOB_SCRIPT

##############################################################
#  Move files back to session directory (job is done on node only)
#  RUNTIME_JOB_DIR -> RUNTIME_LOCAL_SCRATCH_DIR/job_id
# !!!!!!!!!!!!!!!!!!! would be better to know the names of files !!!!!!!!!!!
##############################################################
cat >> $PBS_JOB_SCRIPT <<'EOSCR'
if [ ! -z "$RUNTIME_LOCAL_SCRATCH_DIR" ] && [ ! -z "$RUNTIME_NODE_SEES_FRONTEND" ] ; then
  if [ ! -z "$RUNTIME_FRONTEND_SEES_NODE" ] ; then
    # just move it
    rm "$RUNTIME_FRONTEND_JOB_DIR"
    mv "$RUNTIME_NODE_JOB_DIR" `dirname "$RUNTIME_FRONTEND_JOB_DIR"`
  else
    # remove links
    rm "$RUNTIME_JOB_STDOUT" 2>/dev/null
    rm "$RUNTIME_JOB_STDERR" 2>/dev/null
    # move whole directory
    cp -pR "$RUNTIME_NODE_JOB_DIR" `dirname "$RUNTIME_FRONTEND_JOB_DIR"`
    rm -rf "$RUNTIME_NODE_JOB_DIR"
  fi
fi
echo "exitcode=$RESULT" >> "$RUNTIME_JOB_DIAG"
exit $RESULT
EOSCR

#######################################
#  Submit the job
#######################################
echo "PBS job script built" 1>&2
# Execute qsub command
cd "$joboption_directory"
echo "PBS script follows:" 1>&2
cat "$PBS_JOB_SCRIPT" 1>&2
echo "" 1>&2
${PBS_QSUB} < $PBS_JOB_SCRIPT 1>$PBS_JOB_OUT 2>$PBS_JOB_ERR
if [ $? -eq '0' ] ; then
   job_id=`cat $PBS_JOB_OUT | awk '{split($0,field,".");print field[1]"."field[2]}'`
   if [ "${job_id}" = "" ] ; then
      echo "job *NOT* submitted successfully!" 1>&2
      echo "failed getting the pbs jobid for the job!" 1>&2
   else
      echo "joboption_jobid=$job_id" >> $arg_file
      echo "job submitted successfully!" 1>&2
      echo "local job id: $job_id" 1>&2
      # Remove temporary job script file
      rm -f $PBS_JOB_SCRIPT $PBS_JOB_OUT $PBS_JOB_ERR
      echo "----- exiting submit_pbs_job -----" 1>&2
      echo "" 1>&2
      exit 0
   fi
else
  echo "job *NOT* submitted successfully!" 1>&2
  echo "got error code from qsub!" 1>&2
fi
echo "Output is:" 1>&2
cat $PBS_JOB_OUT 1>&2
echo "Error output is:"
cat $PBS_JOB_ERR 1>&2
rm -f $PBS_JOB_SCRIPT $PBS_JOB_OUT $PBS_JOB_ERR
echo "----- exiting submit_pbs_job -----" 1>&2
echo "" 1>&2
exit 1
