nordugrid-arc-arex 5.0.5-1ubuntu1 / usr / share / arc / scan-pbs-job

#!/bin/sh
#
#   Periodically read log files of PBS and put mark files
# for job, which finished.
#   If log files are not available scan for finished (absent) jobs 
# in PBS and put mark files for job, which finished.
#
# usage: scan_pbs_job control_dir ...

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

if [ -z "$1" ] ; then exit 1 ; fi

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

libexecdir="${ARC_LOCATION:-/usr}/lib/arc/"
pkgdatadir="$basedir"

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

# Assume that gm-kick and scan_common is installed in the same directory
GMKICK=${libexecdir}/gm-kick

. "${pkgdatadir}/scan_common.sh" || exit $?

# Where to store temporary files
TMPDIR=${TMPDIR:-/tmp}

# directory containing PBS server logs
pbs_log_dir=${CONFIG_pbs_log_path:-/var/spool/pbs/server_logs}

RUNTIME_NODE_SEES_FRONTEND=$CONFIG_shared_filesystem

#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

# first control_dir is used for storing own files
control_dir=$1
control_dirs=
while [ $# -gt 0 ] ; do
  control_dirs="${control_dirs} \"$1\""
  shift
done

my_id=`id -u`

state_file=$control_dir/pbs_log_scan.`id -un`

lines=`cat "$state_file" 2>/dev/null`
ldt=`echo $lines | awk '{split($0,field," ");print field[1]}' `
lines=`echo $lines | awk '{split($0,field," ");print field[2]}'`
lines_skip=$(( $lines + 0 ))
ldate=$(( $ldt + 0 ))
if [ -z "$lines_skip" ] ; then lines_skip='0' ; fi
if [ -z "$ldate" ] ; then ldate='0' ; fi
whole_line=

find_by_local() {
  eval "set -- $control_dirs"
  for ctr_dir in "$@"; do
    find ${ctr_dir}/processing -name 'job.*.status' -print0 \
    | sed 's/processing\/job\.\([^\.]*\)\.status/job.\1.local/g' \
    | xargs -0 grep -F -l $whole_line "localid=$job_id" 2>/dev/null
  done \
  | head -n 1
}

find_by_grami() {
  eval "set -- $control_dirs"
  for ctr_dir in "$@"; do
    find ${ctr_dir}/processing -name 'job.*.status' -print0 \
    | sed 's/processing\/job\.\([^\.]*\)\.status/job.\1.grami/g' \
    | xargs -0 grep -F -l $whole_line "joboption_jobid=$job_id" 2>/dev/null
  done \
  | sed 's/\.grami$/.local/' \
  | head -n 1
}

# set_job_vars takes a line from pbs logs and splits it, returning information
# in pbs_date, pbs_code, pbs_server, pbs_job, job_id, job_message and rest_line

set_job_vars() {
  pbs_date=$1
  pbs_code=$2
  pbs_server=$3
  pbs_job=$4
  job_id=$5
  job_message=$6
  rest_line=$7
}

#
#  Main function for processing one PBS log.
#  Extracts log lines with code 0010 (job exited) and 0008 (job killed)
#
# TODO this should be split into smaller functions
process_log_file () {
  eval "set -- $control_dirs"

  #we grep for finished jobs, then use sed to remove already processed lines
  #OBS: deleted jobs have a 0008 message with not much info in it. A 0010
  # message may follow (or not) with full usage stats. By this time the
  # job has already been processed, so this info is ignored!
  #TODO: make log scanning more intelligent.
  exited_killed_jobs=`egrep '^[^;]*;0010;[^;]*;Job;|^[^;]*;0008;[^;]*;Job;[^;]*;Exit_status=|^[^;]*;0008;[^;]*;Job;[^;]*;Job deleted' ${lname} | tail -n+$(( $lines_skip + 1 ))`

  #TODO should we add processed lines before jobs have actually been processed? What if the last job only has half a record?
  new_lines=`echo "$exited_killed_jobs" | wc -l`
  # new_lines set to 1 when string is empty, should have been 0
  [ "x$exited_killed_jobs" = x ] &&  continue

  lines_processed=$(( $lines_skip + $new_lines ))

  if [ "$lines_processed" -lt '0' ] ; then
    lines_processed=0;
  fi

  echo "$cname $lines_processed"> $state_file

  exited_killed_jobs=`echo "$exited_killed_jobs" | sort -u`

  # force word splitting to happen only on newlines
  old_IFS=$IFS; IFS='
'
  for job in $exited_killed_jobs; do

    # Split line into fields by forcing word splitting to happen on ";" 
    IFS=";"
    set_job_vars $job
    IFS=$old_IFS

    # Try to extract exit code of PBS (note: if executable fails it's code goes to PBS)
    exit_code=`echo "$job_message" | sed -n 's/^.*Exit_status=\([-0-9]*\).*/\1/p'`

    # Check if job has suffix
    echo "$job_id" | grep -q -F .
    if [ ! $? = '0' ] ; then 
      whole_line=-x
    else
      job_id=`echo "$job_id" | awk '{split($0,field,".");print field[1]"."field[2]}'`
      whole_line=
    fi

    # look for this id in job.ID.local, then in job.ID.grami
    name=`find_by_local`
    if [ -z "$name" ]; then
      name=`find_by_grami`
      if [ -z "$name" ]; then continue; fi
    fi
    if [ "$my_id" != '0' ] ; then
      if [ ! -O "$name" ] ; then continue ; fi
    fi
    uid=$(get_owner_uid "$name")
    [ -z "$uid" ] && { log "Failed to stat $name"; continue; }

    base_name=`echo "$name" 2>/dev/null | sed -n 's/\.local$//p'`
    if [ -z "${base_name}" ] ; then continue ; fi

    # check if job already reported
    if [ -f "${base_name}.lrms_done" ] ; then continue ; fi

    statusfile=`echo "$name" 2>/dev/null | sed -n 's/job\.\([^\.]*\)\.local$/processing\/job.\1.status/p'`

    # more protection - check if grid-manager thinks job is still running
    egrep 'INLRMS|SUBMIT|CANCELING' "$statusfile" >/dev/null 2>&1
    if [ ! $? = '0' ] ; then continue ; fi

    # So far only PBS exit code is available
    # It would be nice to have exit code of main executable
    exitcode=''

    # get session directory of this job
    sessiondir=`grep -h '^sessiondir=' "${base_name}.local" | sed 's/^sessiondir=\(.*\)/\1/'`
    diagfile="${sessiondir}.diag"
    commentfile="${sessiondir}.comment"

    if [ -z "$sessiondir" ] ; then
      log "Failed to determine the path of the job's session directory"
    else
      # have chance to obtain exit code
      if [ -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
        # In case of non-NFS setup it may take some time till
        # diagnostics file is delivered. Wait for it max 2 minutes.
        # OBS: exitcode may never appear in the .diag file if the job was
        # killed. There will be a 2 minute delay for every such job!
        diag_tries=0
        while [ "$diag_tries" -lt 20 ] ; do
          job_read_diag # uses $sessiondir, $uid
          if [ ! -z "$exitcode" ] ; then break ; fi
          sleep 10
          diag_tries=$(( $diag_tries + 1 ))
          log "no exitcode in diag file $diagfile (try $diag_tries of 20)"
        done
      else
        job_read_diag # uses $sessiondir, $uid
      fi
    fi
    # Try to obtain message from PBS if any
    pbs_comment=$(do_as_uid "$uid" "tail -n 1 '$commentfile'")
    save_commentfile "$uid" "$commentfile" "${base_name}.errors"

    # Extract values from PBS
    walltime=`echo "$job_message" | sed -n 's/^.*resources_used.walltime=\(\([0-9]*:\)*[0-9][0-9]\).*/\1/p'`
    cputime=`echo "$job_message" | sed -n 's/^.*resources_used.cput=\(\([0-9]*:\)*[0-9][0-9]\).*/\1/p'`
    mem=`echo "$job_message" | sed -n 's/^.*resources_used.mem=\([0-9]*\)kb.*/\1/p'`
    vmem=`echo "$job_message" | sed -n 's/^.*resources_used.vmem=\([0-9]*\)kb.*/\1/p'`

    # Convert to utc and store as seconds
    date_to_utc_seconds "$pbs_date"
    if [ ! -z "$return_date_seconds" ]; then
      # Convert from seconds to YYYYMMDDHHMMSSZ
      seconds_to_mds_date "$return_date_seconds"
      endtime=$return_mds_date
      # Find out how many seconds the job executed
      interval_to_seconds "$walltime"
      if [ ! -z "$return_interval_seconds" ]; then
        # Convert from seconds to YYYYMMDDHHMMSSZ
        seconds_to_mds_date $(( $return_date_seconds - $return_interval_seconds ))
        starttime=$return_mds_date
      fi
    fi

    # Values to write to diag. These will override values already written.
    interval_to_seconds "$walltime"
    [ -n "$return_interval_seconds" ] && WallTime=$return_interval_seconds
    interval_to_seconds "$cputime"
    [ -n "$return_interval_seconds" ] && UserTime=$return_interval_seconds
    [ -n "$return_interval_seconds" ] && KernelTime=0
    [ -n "$mem" ]                     && UsedMemory=$mem
    [ -n "$vmem" ]                    && TotalMemory=$vmem
    [ -n "$starttime" ]               && LRMSStartTime=$starttime
    [ -n "$endtime" ]                 && LRMSEndTime=$endtime
    [ -n "$pbs_comment" ]             && LRMSMessage=$pbs_comment
    [ -n "$exit_code" ]               && LRMSExitcode=$exit_code
    job_write_diag

    if [ -z "$exitcode" ] ; then
      # No exit code of job means job was most probably killed
      if [ -z "$exit_code" ] ; then exit_code='-1'; fi
      if [ "$exit_code" = '0' ] ; then
        echo "Job $job_id failed but PBS have not noticed that" 1>&2
        echo "-1 Job failed but PBS reported 0 exit code." > "${base_name}.lrms_done"
      elif [ -z "$pbs_comment" ] ; then
        echo "Job $job_id failed with PBS exit code $exit_code" 1>&2
        echo "$exit_code Job was killed by PBS." > "${base_name}.lrms_done"
      else
        echo "Job $job_id failed with PBS exit code $exit_code" 1>&2
        echo "$exit_code $pbs_comment" > "${base_name}.lrms_done"
      fi
    else
      if [ -z "$exit_code" ] ; then exit_code='-1'; fi
      if [ ! "$exitcode" = 0 ] ; then
        if [ "$exit_code" = '0' ] ; then exit_code='-1'; fi
        echo "Job $job_id failed with exit code $exitcode, PBS reported $exit_code." 1>&2
        echo "$exit_code Job failed with exit code $exitcode." > "${base_name}.lrms_done"
      else
        if [ ! "$exit_code" = '0' ] ; then
          echo "Job finished properly but PBS reported $exit_code." 1>&2
          if [ -z "$pbs_comment" ] ; then
            echo "$exit_code Job was killed by PBS." > "${base_name}.lrms_done"
          else
            echo "$exit_code $pbs_comment" > "${base_name}.lrms_done"
          fi
        else
          # echo "Job finished without errors." 1>&2
          echo "0" > "${base_name}.lrms_done"
        fi
      fi
    fi
    # wake up GM
    ${GMKICK} "${base_name}.local"
  done
  IFS=$old_IFS
}

readable_logs=no
# Check $pbs_log_dir for readable files
# if any are found, process them and update relevant information
if [ ! -z "${pbs_log_dir}" ] ; then
for cname in `ls -1 ${pbs_log_dir}/ 2>/dev/null | grep '^[0-9]*$'` ; do
  lname="${pbs_log_dir}/$cname"
  if [ ! -r "$lname" ] ; then continue ; fi
  readable_logs=yes
  if [ "$cname" -lt "$ldate" ] ; then
    continue
  elif [ "$cname" -gt "$ldate" ] ; then
    lines_skip=0
  fi
  echo "Date: " $cname
  last_modified=`stat $lname | grep Modify`
  process_log_file
done
fi

# main loop, stay here up to 60 seconds if log is still updated while
# we are reading it.
if [ "$readable_logs" = 'yes' ] ; then
  time_count=0
  while true ; do
    new_modified=`stat $lname | grep Modify`
    if [ "$new_modified" != "$last_modified" ] ; then
      last_modified="$new_modified"
      lines=`cat "$state_file" 2>/dev/null`
      ldt=`echo $lines | awk '{split($0,field," ");print field[1]}' `
      lines=`echo $lines | awk '{split($0,field," ");print field[2]}'`
      lines_skip=$(( $lines + 0 ))
      ldate=$(( $ldt + 0 ))
      process_log_file
    fi
    sleep 10
    time_count=$(( $time_count + 1 ))
    if [ "$time_count" -gt 60 ] ; then break ; fi
  done
  exit 0
fi

# If no PBS logs found try ordinary 'qstat'
eval "set -- $control_dirs"
# Get all running jobs

pidslist=`mktemp "$TMPDIR/qstat.XXXXXX"` || 
if [ ! "$?" = '0' ] ; then
  # FS problems ?
  # TODO debug output here
  sleep 60
  exit 1
fi
${PBS_BIN_PATH}/qstat -a 2>/dev/null 1>"$pidslist"
if [ ! "$?" = '0' ] ; then
  rm -f "$pidslist"
  # PBS server down ?
  sleep 60
  exit 1
fi

exclude_completed () {
  awk '$10!="C"{print $0}'
}

pids=`cat "$pidslist" | grep '^[0-9][0-9]*\.' | exclude_completed | sed 's/^\([0-9][0-9]*\).*/\1/'`
rm -f "$pidslist"
# Go through directories
for ctr_dir in "$@" ; do
  # Obtain ids stored in job.*.local
  ids=`find ${ctr_dir}/processing -name 'job.*.status' -print0 \
       | sed 's/processing\/job\.\([^\.]*\)\.status/job.\1.local/g' \
       | xargs -0 grep -h "^localid=" 2>/dev/null | sed 's/^localid=\([0-9]*\).*/\1/'`
  if [ -z "$ids" ] ; then continue ; fi
  # compare them to running jobs and find missing
  bids=
  for id in $ids ; do
    found=`echo "$pids" | grep "^$id$"`
    if [ -z "$found" ] ; then
      bids="$bids $id"
    fi
  done
  # go through missing ids
  for id in $bids ; do
    # find grid job corresponding to curent local id
    jobfile=`find ${ctr_dir}/processing -name 'job.*.status' -print0 \
             | sed 's/processing\/job\.\([^\.]*\)\.status/job.\1.local/g' \
             | xargs -0 grep -F -l "localid=$id." 2>/dev/null`
    if [ -z "$jobfile" ] ; then continue ; fi
    if [ "$my_id" != '0' ] ; then
      if [ ! -O "$jobfile" ] ; then continue ; fi
    fi
    uid=$(get_owner_uid "$jobfile")
    [ -z "$uid" ] && { log "Failed to stat $jobfile"; continue; }
    # extract grid id
    gridid=`basename "$jobfile" '.local' | sed 's/^job\.//'`
    donefile="${ctr_dir}/job.${gridid}.lrms_done"
    if [ -f "$donefile" ] ; then continue ; fi
    statusfile="${ctr_dir}/processing/job.${gridid}.status"
    if [ ! -f "$statusfile" ] ; then continue ; fi
    status=`cat "$statusfile"`
    if [ "$status" != "INLRMS" ] && [ "$status" != "CANCELING" ]; then continue ; fi

    # get session directory of this job
    session=`grep -h '^sessiondir=' "$jobfile" | sed 's/^sessiondir=\(.*\)/\1/'`
    if [ ! -z "$session" ] ; then
      # have chance to obtain exit code
      diagfile="${session}.diag"
      if [ ! -z "$session" ] ; then
        # have chance to obtain exit code
        exitcode=$(do_as_uid "$uid" "grep '^exitcode=' '$diagfile'" | sed 's/^exitcode=//')
      fi
      if [ ! -z "$exitcode" ] ; then
        # job finished and exit code is known
        save_commentfile "$uid" "${session}.comment" "${ctr_dir}/job.${gridid}.errors"
        echo "$exitcode Executable finished with exit code $exitcode" > "$donefile"
        ${GMKICK} "$jobfile"
        echo "Job $gridid finished with exit code $exitcode"
        continue
      fi
    fi
    # job has probaly finished and exit code is not known
    exitcode='-1'
    countfile="${ctr_dir}/job.${gridid}.lrms_job"
    counter=0
    if [ -f "$countfile" ] ; then
      counter=`cat "$countfile"`
      counter=$(( $counter + 1 ))
    fi
    if [ "$counter" -gt 5 ] ; then
      rm -f "$countfile"
      save_commentfile "$uid" "${session}.comment" "${ctr_dir}/job.${gridid}.errors"
      echo "$exitcode Job was lost with unknown exit code" > "$donefile"
      ${GMKICK} "$jobfile"
      echo "Job $gridid finished with unknown exit code"
    else
      echo "$counter" > "$countfile"
    fi
  done
  # go through existing ids
  for id in $pids ; do
    # find grid job corresponding to curent local id
    jobfile=`find ${ctr_dir} -name 'job.*.local' -print0 | xargs -0 grep -F -l "localid=$id." 2>/dev/null`
    if [ -z "$jobfile" ] ; then continue ; fi
    gridid=`basename "$jobfile" '.local' | sed 's/^job\.//'`
    countfile="${ctr_dir}/job.${gridid}.lrms_job"
    # reset failure counter
    rm -f "$countfile"
  done
done
sleep 60
exit 0