/usr/share/arc/scan-lsf-job is in nordugrid-arc-arex 4.0.0-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 | #!/bin/sh
#
#
# Scan for finished LSF jobs, using bjobs
#
# usage: scan_lsf_job control_dir ...
# Set variables:
# LSF_BIN_PATH
# 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 $?
libexecdir="${ARC_LOCATION:-/usr}/lib/arc/"
pkgdatadir="$basedir"
# Assume that gm-kick is installed in the same directory
GMKICK=${libexecdir}/gm-kick
. "${pkgdatadir}/configure-lsf-env.sh" || exit $?
. "${pkgdatadir}/scan_common.sh" || exit $?
umask 022
if [ -z "$1" ] ; then
echo "Missing Input Script file as arg1" 1>&2
exit 1 ;
fi
# first control_dir is used for storing own files
echo `date`" : control_dir=$1" 1>&2
control_dir=$1
control_dirs=
while [ $# -gt 0 ] ; do
control_dirs="${control_dirs} $1"
shift
done
my_id=`id -u`
# Get all running jobs
#
if [ -z ${LSF_BIN_PATH} ]; then
echo "${LSF_BIN_PATH} not set" 1>&2
exit 1
fi
lsf_stat=`${LSF_BIN_PATH}/bjobs -a -u all 2>/dev/null` # | grep RUN | grep '^ [:digit:]'
if [ -z "${lsf_stat}" ] ; then
echo "bjobs returned empty result" 1>&2
fi
pids=`echo "${lsf_stat}" | egrep 'PSUSP|USUSP|SSUSP|RUN|PEND' | sed -e 's/^\([^ ]*\).*/\1/'`
eval "set -- $control_dirs"
# Go through directories
for ctr_dir in $control_dir ; 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
# 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
if [ "$my_id" != '0' ] ; then
if [ ! -O "$jobfile" ] ; then continue ; fi
fi
uid=$(get_owner_uid "$jobfile")
[ -z "$uid" ] && { log "Failed to stat $jobfile"; continue; }
# get session directory of this job
sessiondir=`grep -h '^sessiondir=' "$jobfile" | sed 's/^sessiondir=\(.*\)/\1/'`
# get job specific output and remove header
bjobs_output="`${LSF_BIN_PATH}/bjobs -W -w $id 2>/dev/null | sed -e'1,1d'`"
job_status="`echo $bjobs_output | awk '{print $3}'`"
# DONE if exit_code is 0, EXIT if non zero
if [ "${job_status}" = "DONE" ] || [ "${job_status}" = "EXIT" ]; then
job_read_diag
starttime="`echo $bjobs_output | awk '{print $14}' | sed 's/-/ /g'`"
endtime="`echo $bjobs_output | awk '{print $15}' | sed 's/-/ /g'`"
date_to_utc_seconds "$starttime"
starttime_seconds="$return_date_seconds"
seconds_to_mds_date "$return_date_seconds"
LRMSStartTime=$return_mds_date
date_to_utc_seconds "$endtime"
endtime_seconds="$return_date_seconds"
seconds_to_mds_date "$return_date_seconds"
LRMSEndTime=$return_mds_date
#TODO handle cputime (walltime * count?) etc.
walltime=$(( $endtime_seconds - $starttime_seconds))
#cputime=$(( $walltime * $count))
# Values to write to diag. These will override values already written.
[ -n "$walltime" ] && WallTime=$walltime
#[ -n "$cputime" ] && UserTime=$cputime
#[ -n "$cputime" ] && KernelTime=0
job_write_diag
fi
if [ -n "$sessiondir" ] ; then
# have chance to obtain exit code
diagfile="${sessiondir}.diag"
if [ -n "$sessiondir" ] ; then
# have chance to obtain exit code
exitcode=$(do_as_uid "$uid" "grep '^exitcode=' '$diagfile'" | sed 's/^exitcode=//')
fi
if [ -n "$exitcode" ] ; then
# job finished and exit code is known
save_commentfile "$uid" "${sessiondir}.comment" "${ctr_dir}/job.${gridid}.errors"
echo "$exitcode Executable finished with exit code $exitcode" > "$donefile"
${GMKICK} "$jobfile"
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" "${sessiondir}.comment" "${ctr_dir}/job.${gridid}.errors"
echo "$exitcode Job was lost with unknown exit code" > "$donefile"
${GMKICK} "$jobfile"
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
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