nordugrid-arc-arex 5.3.0~rc1-1 / usr / share / arc / submit-condor-job

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

echo "----- starting submit_condor_job -----" 1>&2
joboption_lrms=condor

# ARC1 passes first the config file.
if [ "$1" = "--config" ]; then shift; ARC_CONFIG=$1; shift; fi

basedir=`dirname $0`
basedir=`cd $basedir > /dev/null && pwd` || exit $?

pkgdatadir="$basedir"

. ${pkgdatadir}/configure-condor-env.sh || exit $?
. ${pkgdatadir}/submit_common.sh || exit $?

perflogfilesub="${perflogdir}/submission.perflog"

if [ ! -z "$perflogdir" ]; then
   start_ts=`date +%s.%N`
fi

##############################################################
# Parse grami file, read arc config
##############################################################

init $1

read_arc_conf

failures_file="$joboption_controldir/job.$joboption_gridid.failed"

if [ -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
   RUNTIME_LOCAL_SCRATCH_DIR="\${_CONDOR_SCRATCH_DIR}"
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
    echo "Submission: Configuration error.">>"$failures_file"
    exit 1
  fi
fi

##############################################################
# Zero stage of runtime environments
##############################################################
RTE_stage0

##############################################################
# create job script
##############################################################
mktempscript

is_cluster=true
##############################################################
# Start job description file
##############################################################

CONDOR_SUBMIT='condor_submit'
if [ ! -z "$CONDOR_BIN_PATH" ] ; then
  CONDOR_SUBMIT=${CONDOR_BIN_PATH}/${CONDOR_SUBMIT}
fi

# HTCondor job script and submit description file
rm -f "$LRMS_JOB_SCRIPT"
LRMS_JOB_SCRIPT="${joboption_directory}/condorjob.sh"
LRMS_JOB_DESCRIPT="${joboption_directory}/condorjob.jdl"

echo "# HTCondor job description built by grid-manager" > $LRMS_JOB_DESCRIPT
echo "Executable = condorjob.sh" >> $LRMS_JOB_DESCRIPT
echo "Input = $joboption_stdin" >> $LRMS_JOB_DESCRIPT
echo "Log = ${joboption_directory}/log">> $LRMS_JOB_DESCRIPT

# write HTCondor output to .comment file if possible, but handle the situation when
# jobs are submitted by HTCondor-G < 8.0.5
condor_stdout="${joboption_directory}.comment"
condor_stderr="${joboption_directory}.comment"
if [ -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
#   if [[ $joboption_stdout =~ _condor_stdout$ ]]; then
   if expr match "$joboption_stdout" '.*_condor_stdout$' > /dev/null; then
      condor_stdout=$joboption_stdout;
      condor_stderr=$joboption_stderr;
   fi
fi
echo "Output = $condor_stdout">> $LRMS_JOB_DESCRIPT
echo "Error = $condor_stderr">> $LRMS_JOB_DESCRIPT

# queue
if [ ! -z "${joboption_queue}" ] ; then
  echo "+NordugridQueue = $joboption_queue" >> $LRMS_JOB_DESCRIPT
fi

# job name for convenience
if [ ! -z "${joboption_jobname}" ] ; then
    #TODO is this necessary? do parts of the infosys need these limitations?
  jobname=`echo "$joboption_jobname" | \
           sed 's/^\([^[:alpha:]]\)/N\1/' | \
           sed 's/[^[:alnum:]]/_/g' | \
           sed 's/\(...............\).*/\1/'`
  echo "Description = $jobname" >> $LRMS_JOB_DESCRIPT
else
    jobname="gridjob"
    echo "Description = $jobname" >> $LRMS_JOB_DESCRIPT
fi

# environment
echo "GetEnv = True" >> $LRMS_JOB_DESCRIPT

# universe
echo "Universe = vanilla" >> $LRMS_JOB_DESCRIPT

# notification
echo "Notification = Never" >> $LRMS_JOB_DESCRIPT

# requirements
if [ ! -z "$CONFIG_condor_requirements" ] ; then
  echo "Requirements = $CONFIG_condor_requirements" >> $LRMS_JOB_DESCRIPT
fi

#####################################################
# priority
#####################################################
if [ ! -z "$joboption_priority" ]; then
  #Condor uses any integer as priority. 0 being default. Only per user basis.
  #We assume that only grid jobs are relevant.
  #In that case we can use ARC 0-100 but translated so default is 0.
  priority=$((joboption_priority-50))
  echo "Priority = $priority" >> $LRMS_JOB_DESCRIPT
fi

# rank
if [ ! -z "$CONFIG_condor_rank" ] ; then
  echo "Rank = $CONFIG_condor_rank" >> $LRMS_JOB_DESCRIPT
fi

# proxy
echo "x509userproxy = $joboption_controldir/job.$joboption_gridid.proxy" >> $LRMS_JOB_DESCRIPT

##############################################################
# (non-)parallel jobs
##############################################################

set_count

if [ ! -z $joboption_count ] && [ $joboption_count -gt 0 ] ; then
  echo "request_cpus = $joboption_count" >> $LRMS_JOB_DESCRIPT
fi

if [ "$joboption_exclusivenode" = "true" ]; then
  echo "+RequiresWholeMachine=True" >> $LRMS_JOB_DESCRIPT
fi

##############################################################
# Execution times (minutes)
##############################################################

REMOVE="FALSE"

if [ ! -z "$joboption_cputime" ] ; then
  if [ $joboption_cputime -lt 0 ] ; then
    echo 'WARNING: Less than 0 cpu time requested: $joboption_cputime' 1>&2
    joboption_cputime=0
    echo 'WARNING: cpu time set to 0' 1>&2
  fi
  maxcputime=$(( $joboption_cputime / $joboption_count ))
  echo "+JobCpuLimit = $joboption_cputime" >> $LRMS_JOB_DESCRIPT
  REMOVE="${REMOVE} || RemoteUserCpu + RemoteSysCpu > JobCpuLimit"
  
fi  
  
if [ -z "$joboption_walltime" ] ; then
  if [ ! -z "$joboption_cputime" ] ; then
    # Set walltime for backward compatibility or incomplete requests
    joboption_walltime=$(( $maxcputime * $walltime_ratio ))
  fi
fi

if [ ! -z "$joboption_walltime" ] ; then
  if [ $joboption_walltime -lt 0 ] ; then
    echo 'WARNING: Less than 0 wall time requested: $joboption_walltime' 1>&2
    joboption_walltime=0
    echo 'WARNING: wall time set to 0' 1>&2
  fi
  echo "+JobTimeLimit = $joboption_walltime" >> $LRMS_JOB_DESCRIPT
  REMOVE="${REMOVE} || RemoteWallClockTime > JobTimeLimit"
fi

##############################################################
# Requested memory (mb)
##############################################################

set_req_mem

if [ ! -z "$joboption_memory" ] ; then
  memory_bytes=$(( $joboption_memory * 1024 ))
  memory_req=$(( $joboption_memory ))
  # HTCondor needs to know the total memory for the job, not memory per core
  if [ ! -z $joboption_count ] && [ $joboption_count -gt 0 ] ; then
     memory_bytes=$(( $joboption_count * $memory_bytes ))
     memory_req=$(( $joboption_count * $memory_req ))
  fi
  echo "request_memory=$memory_req" >> $LRMS_JOB_DESCRIPT
  echo "+JobMemoryLimit = $memory_bytes" >> $LRMS_JOB_DESCRIPT
  REMOVE="${REMOVE} || ResidentSetSize > JobMemoryLimit"
fi

##############################################################
#  HTCondor stage in/out
##############################################################
if [ -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
  (
    cd "$joboption_directory"
    if [ $? -ne '0' ] ; then
      echo "Can't change to session directory: $joboption_directory" 1>&2
      rm -f "$LRMS_JOB_SCRIPT" "$LRMS_JOB_DESCRIPT" "$LRMS_JOB_OUT" "$LRMS_JOB_ERR"
      echo "Submission: Configuration error.">>"$failures_file"
      exit 1
    fi
    scratch_dir=`dirname "$joboption_directory"`
    echo "should_transfer_files = YES" >> $LRMS_JOB_DESCRIPT
    echo "When_to_transfer_output = ON_EXIT_OR_EVICT" >> $LRMS_JOB_DESCRIPT

    count=0
    input_files="Transfer_input_files = "
    eval "input_file=\$joboption_inputfile_$count"
    while [ -n "${input_file}" ]; do
      if [ "$count" -gt "0" ]; then
          input_files="${input_files},"
      fi
      input_files="${input_files} ${joboption_directory}${input_file}"
      count=$((count+1))
      eval "input_file=\$joboption_inputfile_$count"
    done
    echo "${input_files}" >> $LRMS_JOB_DESCRIPT
  )
fi

echo "Periodic_remove = ${REMOVE}" >> $LRMS_JOB_DESCRIPT
echo "Queue" >> $LRMS_JOB_DESCRIPT

echo "#!/bin/bash -l" > $LRMS_JOB_SCRIPT

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

# Script must have execute permission
chmod 0755 $LRMS_JOB_SCRIPT

sourcewithargs_jobscript

##############################################################
# Add environment variables
##############################################################
add_user_env

##############################################################
# Check for existance of executable,
# there is no sense to check for executable if files are 
# downloaded directly to computing node
##############################################################
if [ -z "${joboption_arg_0}" ] ; then
  echo 'Executable is not specified' 1>&2
  rm -f "$LRMS_JOB_SCRIPT" "$LRMS_JOB_DESCRIPT" "$LRMS_JOB_OUT" "$LRMS_JOB_ERR"
  echo "Submission: Job description error.">>"$failures_file"
  exit 1
fi

#######################################################################
# copy information useful for transfering files to/from node directly
#######################################################################
if [ "$joboption_localtransfer" = 'yes' ] ; then
  setup_local_transfer
fi

######################################################################
# Adjust working directory for tweaky nodes
# RUNTIME_GRIDAREA_DIR should be defined by external means on nodes
######################################################################
if [ ! -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
  setup_runtime_env
else
  echo "RUNTIME_JOB_DIR=$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid" >> $LRMS_JOB_SCRIPT
  echo "RUNTIME_JOB_DIAG=$RUNTIME_LOCAL_SCRATCH_DIR/${joboption_gridid}.diag" >> $LRMS_JOB_SCRIPT
  RUNTIME_STDIN_REL=`echo "${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}\"" >> $LRMS_JOB_SCRIPT
  else
    echo "RUNTIME_JOB_STDIN=\"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$RUNTIME_STDIN_REL\"" >> $LRMS_JOB_SCRIPT
  fi
  if [ "$RUNTIME_STDOUT_REL" = "${joboption_stdout}" ] ; then
    echo "RUNTIME_JOB_STDOUT=\"${joboption_stdout}\"" >> $LRMS_JOB_SCRIPT
  else
    echo "RUNTIME_JOB_STDOUT=\"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$RUNTIME_STDOUT_REL\"" >> $LRMS_JOB_SCRIPT
  fi
  if [ "$RUNTIME_STDERR_REL" = "${joboption_stderr}" ] ; then
    echo "RUNTIME_JOB_STDERR=\"${joboption_stderr}\"" >> $LRMS_JOB_SCRIPT
  else
    echo "RUNTIME_JOB_STDERR=\"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$RUNTIME_STDERR_REL\"" >> $LRMS_JOB_SCRIPT
  fi
fi

##############################################################
# Add std... to job arguments
##############################################################
include_std_streams

##############################################################
#  Move files to local working directory (job is done on node only)
#  RUNTIME_JOB_DIR -> RUNTIME_LOCAL_SCRATCH_DIR/job_id
##############################################################
move_files_to_node

echo "" >> $LRMS_JOB_SCRIPT
echo "RESULT=0" >> $LRMS_JOB_SCRIPT
echo "" >> $LRMS_JOB_SCRIPT

if [ -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
    echo "# move input files to local working directory" >> $LRMS_JOB_SCRIPT
    count=0
    eval "input_file=\$joboption_inputfile_$count"
    while [ -n "${input_file}" ]; do
      echo "mv .${input_file} ${joboption_gridid}/." >> $LRMS_JOB_SCRIPT
      count=$((count+1))
      eval "input_file=\$joboption_inputfile_$count"
    done
fi

#####################################################
#  Download input files
####################################################
download_input_files

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

##############################################################
#  Runtime configuration at computing node
##############################################################
RTE_stage1

##############################################################
#  Diagnostics
##############################################################
echo "echo \"runtimeenvironments=\$runtimeenvironments\" >> \"\$RUNTIME_JOB_DIAG\"" >> $LRMS_JOB_SCRIPT
cat >> $LRMS_JOB_SCRIPT <<'EOSCR'
EOSCR

##############################################################
#  Check intermediate result again
##############################################################
echo "if [ \"\$RESULT\" = '0' ] ; then" >> $LRMS_JOB_SCRIPT

##############################################################
#  Execution
##############################################################
cd_and_run

##############################################################
#  End of RESULT checks
##############################################################
echo "fi" >> $LRMS_JOB_SCRIPT
echo "fi" >> $LRMS_JOB_SCRIPT

##############################################################
#  Runtime (post)configuration at computing node
##############################################################
configure_runtime

#####################################################
#  Upload output files
####################################################
if [ "$joboption_localtransfer" = 'yes' ] ; then
  upload_output_files
else
# There is no sense to keep trash till GM runs uploader
  echo 'if [ ! -z  "$RUNTIME_LOCAL_SCRATCH_DIR" ] ; then' >> $LRMS_JOB_SCRIPT
# Delete all files except listed in job.#.output
  echo '  find ./ -type l -exec rm -f "{}" ";"' >> $LRMS_JOB_SCRIPT
  echo '  find ./ -type f -exec chmod u+w "{}" ";"' >> $LRMS_JOB_SCRIPT

  if [ -f "$joboption_controldir/job.$joboption_gridid.output" ] ; then
    cat "$joboption_controldir/job.$joboption_gridid.output" | \
    # remove leading backslashes, if any
    sed 's/^\/*//' | \
    # backslashes and spaces are escaped with a backslash in job.*.output. The
    # shell built-in read undoes this escaping.
    while read name rest; do

      # make it safe for shell by replacing single quotes with '\''
      name=`printf "%s" "$name"|sed "s/'/'\\\\\\''/g"`;

      # protect from deleting output files including those in the dynamic list
      if [ "${name#@}" != "$name" ]; then     # Does $name start with a @ ?

        dynlist=${name#@}
        echo "  dynlist='$dynlist'" >> $LRMS_JOB_SCRIPT
        cat >> $LRMS_JOB_SCRIPT <<'EOSCR'
  chmod -R u-w "./$dynlist" 2>/dev/null
  cat "./$dynlist" | while read name rest; do
    chmod -R u-w "./$name" 2>/dev/null
  done
EOSCR
      else

        echo "  chmod -R u-w \"\$RUNTIME_JOB_DIR\"/'$name' 2>/dev/null" >> $LRMS_JOB_SCRIPT
        if [ -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
           echo "  mv \"\$RUNTIME_JOB_DIR\"/'$name' ../." >> $LRMS_JOB_SCRIPT
        fi
      fi
    done
  fi

  echo '  find ./ -type f -perm /200 -exec rm -f "{}" ";"' >> $LRMS_JOB_SCRIPT
  echo '  find ./ -type f -exec chmod u+w "{}" ";"' >> $LRMS_JOB_SCRIPT
  echo 'fi' >> $LRMS_JOB_SCRIPT
fi
echo "" >> $LRMS_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 !!!!!!!!!!!
##############################################################
move_files_to_frontend


if [ ! -z "$perflogdir" ]; then
   stop_ts=`date +%s.%N`
   t=`awk "BEGIN { printf \"%.3f\", ${stop_ts}-${start_ts} }"`
   echo "[`date +%Y-%m-%d\ %T`] submit-condor-job, JobScriptCreation: $t" >> $perflogfilesub
fi

#######################################
#  Submit the job
#######################################
echo "HTCondor job script built" 1>&2
# Execute condor_submit command
cd "$joboption_directory"
echo "HTCondor script follows:" 1>&2
echo "-------------------------------------------------------------------" 1>&2
cat "$LRMS_JOB_SCRIPT" 1>&2
echo "-------------------------------------------------------------------" 1>&2
echo "" 1>&2
CONDOR_RESULT=1
CONDOR_TRIES=0
while [ "$CONDOR_TRIES" -lt '10' ] ; do
  if [ ! -z "$perflogdir" ]; then
    start_ts=`date +%s.%N`
  fi

  ${CONDOR_SUBMIT} $LRMS_JOB_DESCRIPT 1>$LRMS_JOB_OUT 2>$LRMS_JOB_ERR
  CONDOR_RESULT="$?"
  
  if [ ! -z "$perflogdir" ]; then
    stop_ts=`date +%s.%N`
    t=`awk "BEGIN { printf \"%.3f\", ${stop_ts}-${start_ts} }"`
    echo "[`date +%Y-%m-%d\ %T`] submit-condor-job, JobSubmission: $t" >> $perflogfilesub
  fi

  if [ "$CONDOR_RESULT" -eq '0' ] ; then break ; fi
  CONDOR_TRIES=$(( $CONDOR_TRIES + 1 ))
  sleep 2
done
if [ $CONDOR_RESULT -eq '0' ] ; then
   job_out=`cat $LRMS_JOB_OUT`
   
   if [ "${job_out}" = "" ]; then
      echo "job *NOT* submitted successfully!" 1>&2
      echo "failed getting the condor jobid for the job!" 1>&2
      echo "Submission: Local submission client behaved unexpectedly.">>"$failures_file"
   elif [ `echo "${job_out}" | grep -Ec "submitted to cluster\s[0-9]+"` != "1" ]; then
      echo "job *NOT* submitted successfully!" 1>&2
      echo "badly formatted condor jobid for the job !" 1>&2
      echo "Submission: Local submission client behaved unexpectedly.">>"$failures_file"
   else
      job_id=`echo $job_out | grep cluster | awk '{print $8}' | sed 's/[\.]//g'`
      hostname=`hostname -f`
      echo "joboption_jobid=${job_id}.${hostname}" >> $arg_file
      echo "condor_log=${joboption_directory}/log" >> $arg_file
      echo "job submitted successfully!" 1>&2
      echo "local job id: $job_id" 1>&2
      # Remove temporary files
      rm -f $LRMS_JOB_OUT $LRMS_JOB_ERR
      echo "----- exiting submit_condor_job -----" 1>&2
      echo "" 1>&2
      exit 0
   fi
else
  echo "job *NOT* submitted successfully!" 1>&2
  echo "got error code from condor_submit: $CONDOR_RESULT !" 1>&2
  echo "Submission: Local submission client failed.">>"$failures_file"
fi
echo "Output is:" 1>&2
cat $LRMS_JOB_OUT 1>&2
echo "Error output is:"
cat $LRMS_JOB_ERR 1>&2
rm -f "$LRMS_JOB_OUT" "$LRMS_JOB_ERR"
echo "----- exiting submit_condor_job -----" 1>&2
echo "" 1>&2
exit 1