/usr/share/arc/submit-SLURM-job is in nordugrid-arc-arex 5.3.0~rc1-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# set -x
#
# Based on globus submission script for pbs
#
# Submits job to SLURM.
# 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_slurm_job -----" 1>&2
joboption_lrms=SLURM
# 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-SLURM-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
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 script
##############################################################
echo "#!/bin/bash -l" > $LRMS_JOB_SCRIPT
echo "# SLURM batch job script built by grid-manager" >> $LRMS_JOB_SCRIPT
# rerun is handled by GM, do not let SLURM requeue jobs itself.
echo "#SBATCH --no-requeue" >> $LRMS_JOB_SCRIPT
# write SLURM output to 'comment' file
echo "#SBATCH -e ${joboption_directory}.comment">> $LRMS_JOB_SCRIPT
echo "#SBATCH -o ${joboption_directory}.comment">> $LRMS_JOB_SCRIPT
echo "" >> $LRMS_JOB_SCRIPT
# choose queue
if [ ! -z "${joboption_queue}" ] ; then
echo "#SBATCH -p $joboption_queue" >> $LRMS_JOB_SCRIPT
fi
##############################################################
# priority
##############################################################
if [ ! -z "$joboption_priority" ]; then
#Slurm priority is -10000 to 10000. Lower is better.
#Default is 0, and only superusers can assign priorities
#less than 0.
#We set the priority as 100 - arc priority.
#This will have the desired effect for all grid jobs
#Local jobs will unfortunatly have a default priority equal
#to ARC priority 100, but there is no way around that.
priority=$((100-joboption_priority))
echo "#SBATCH --nice=${priority}" >> $LRMS_JOB_SCRIPT
else
#If priority is not set we should set it to
#50 to match the default in the documentation
priority=50
echo "#SBATCH --nice=${priority}" >> $LRMS_JOB_SCRIPT
fi
# project name for accounting
if [ ! -z "${joboption_rsl_project}" ] ; then
echo "#SBATCH -U $joboption_rsl_project" >> $LRMS_JOB_SCRIPT
fi
# job name for convenience
if [ ! -z "${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 "#SBATCH -J '$jobname'" >> $LRMS_JOB_SCRIPT
else
jobname="gridjob"
echo "#SBATCH -J '$jobname'" >> $LRMS_JOB_SCRIPT
fi
echo "SLURM jobname: $jobname" 1>&2
# Set up the user's environment on the compute node where the script
# is executed.
echo "#SBATCH --get-user-env=10L" >> $LRMS_JOB_SCRIPT
##############################################################
# (non-)parallel jobs
##############################################################
set_count
nodes_string="#SBATCH -n ${joboption_count}"
echo "$nodes_string" >> $LRMS_JOB_SCRIPT
if [ ! -z $joboption_countpernode ] && [ $joboption_countpernode -gt 0 ] ; then
echo "#SBATCH --ntasks-per-node $joboption_countpernode" >> $LRMS_JOB_SCRIPT
fi
nodes_string="#SBATCH "
i=0
eval "var_is_set=\${joboption_nodeproperty_$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" >> $LRMS_JOB_SCRIPT
if [ "$joboption_exclusivenode" = "true" ]; then
echo "#SBATCH --exclusive" >> $LRMS_JOB_SCRIPT
fi
##############################################################
# Execution times (minutes)
##############################################################
if [ ! -z "$joboption_cputime" ] ; then
if [ $joboption_cputime -lt 0 ] ; then
echo 'WARNING: Less than 0 cpu time requested: $joboption_cputime' 1>&2
joboption_cputime=0
echo 'WARNING: cpu time set to 0' 1>&2
fi
# this is actually walltime deduced from cputime !
maxcputime=$(( $joboption_cputime / $joboption_count ))
cputime_min=$(( $maxcputime / 60 ))
cputime_sec=$(( $maxcputime - $cputime_min * 60 ))
echo "#SBATCH -t ${cputime_min}:${cputime_sec}" >> $LRMS_JOB_SCRIPT
fi
if [ -z "$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: $joboption_walltime' 1>&2
joboption_walltime=0
echo 'WARNING: wall time set to 0' 1>&2
fi
maxwalltime="$joboption_walltime"
walltime_min=$(( $maxwalltime / 60 ))
walltime_sec=$(( $maxwalltime - $walltime_min * 60 ))
echo "#SBATCH -t ${walltime_min}:${walltime_sec}" >> $LRMS_JOB_SCRIPT
fi
##############################################################
# Requested memory (mb)
##############################################################
set_req_mem
if [ ! -z "$joboption_memory" ] ; then
echo "#SBATCH --mem-per-cpu=${joboption_memory}" >> $LRMS_JOB_SCRIPT
fi
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 " " >> $LRMS_JOB_SCRIPT
sourcewithargs_jobscript
##############################################################
# Add environment variables
##############################################################
add_user_env
##############################################################
# Check for existance of executable,
# there is no sense to check for executable if files are
# downloaded directly to computing node
##############################################################
if [ -z "${joboption_arg_0}" ] ; then
echo 'Executable is not specified' 1>&2
rm -f "$LRMS_JOB_SCRIPT" "$LRMS_JOB_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
#####################################################
# 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 >> $LRMS_JOB_SCRIPT <<'EOSCR'
if [ ! "X$SLURM_NODEFILE" = 'X' ] ; then
if [ -r "$SLURM_NODEFILE" ] ; then
cat "$SLURM_NODEFILE" | sed 's/\(.*\)/nodename=\1/' >> "$RUNTIME_JOB_DIAG"
NODENAME_WRITTEN="1"
else
SLURM_NODEFILE=
fi
fi
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
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 "" >> $LRMS_JOB_SCRIPT
##############################################################
# Move files back to session directory (job is done on node only)
# RUNTIME_JOB_DIR -> RUNTIME_LOCAL_SCRATCH_DIR/job_id
# !!!!!!!!!!!!!!!!!!! would be better to know the names of files !!!!!!!!!!!
##############################################################
move_files_to_frontend
#######################################
# Submit the job
#######################################
echo "SLURM job script built" 1>&2
# Execute sbatch command
cd "$joboption_directory"
echo "SLURM script follows:" 1>&2
echo "-------------------------------------------------------------------" 1>&2
cat "$LRMS_JOB_SCRIPT" 1>&2
echo "-------------------------------------------------------------------" 1>&2
echo "" 1>&2
SLURM_RESULT=1
SLURM_TRIES=0
#job creation finished
if [ ! -z "$perflogdir" ]; then
stop_ts=`date +%s.%N`
t=`awk "BEGIN { printf \"%.3f\", ${stop_ts}-${start_ts} }"`
echo "[`date +%Y-%m-%d\ %T`] submit-slurm-job, JobScriptCreation: $t" >> $perflogfilesub
fi
while [ "$SLURM_TRIES" -lt '10' ] ; do
# Unset all environment variables before calling sbatch. Otherwise
# SLURM will forward them to the job and leak information about
# the grid-manager.
# Only unset lines with assignments.
# Risks unsetting variables in sub assignments, but this is likely harmless.
# TODO: Maybe we only should unset $ARC_*, $CONFIG_*, $GLOBUS_* etc?
if [ ! -z "$perflogdir" ]; then
start_ts=`date +%s.%N`
fi
(for i in $(env|grep '^[A-Za-z][A-Za-z0-9]*='|grep -v "LRMS_JOB_SCRIPT"|cut -d= -f1);do unset $i;done; \
${sbatch} $LRMS_JOB_SCRIPT) 1>$LRMS_JOB_OUT 2>$LRMS_JOB_ERR
SLURM_RESULT="$?"
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-slurm-job, JobSubmission: $t" >> $perflogfilesub
fi
if [ "$SLURM_RESULT" -eq '0' ] ; then break ; fi
if [ "$SLURM_RESULT" -eq '198' ] ; then
echo "Waiting for queue to decrease" 1>&2
sleep 60
SLURM_TRIES=0
continue
fi
grep 'maximum number of jobs' "$LRMS_JOB_OUT" "$LRMS_JOB_ERR"
if [ $? -eq '0' ] ; then
echo "Waiting for queue to decrease" 1>&2
sleep 60
SLURM_TRIES=0
continue
fi
# A rare SLURM error, but may cause chaos in the information/accounting system
grep 'unable to accept job' "$LRMS_JOB_OUT" "$LRMS_JOB_ERR"
if [ $? -eq '0' ] ; then
echo "Waiting for queue to decrease" 1>&2
sleep 60
SLURM_TRIES=0
continue
fi
SLURM_TRIES=$(( $SLURM_TRIES + 1 ))
sleep 2
done
if [ $SLURM_RESULT -eq '0' ] ; then
#TODO test what happens when the jobqueue is full or when the slurm ctld is not responding
# SLURM 1.x and 2.2.x outputs the jobid into STDERR and STDOUT respectively. Concat them,
# and let sed sort it out. From the exit code we know that the job was submitted, so this
# is safe. Ulf Tigerstedt <tigerste@csc.fi> 1.5.2011
# This is unfortunately not safe. Cray's SLURM sbatch returns 0, when it fails to submit a job. <soettrup@nbi.dk> 22.1.2015
job_id=`cat $LRMS_JOB_OUT $LRMS_JOB_ERR |sed -e 's/^\(sbatch: \)\{0,1\}Submitted batch job \([0-9]*\)$/\2/'`
if expr match "${job_id}" '[0-9][0-9]*' >/dev/null; then
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 $LRMS_JOB_SCRIPT $LRMS_JOB_OUT $LRMS_JOB_ERR
echo "----- exiting submit_slurm_job -----" 1>&2
echo "" 1>&2
exit 0
else
echo "job *NOT* submitted successfully!" 1>&2
echo "failed getting the slurm jobid for the job!" 1>&2
echo "Instead got: ${job_id}" 1>&2
echo "Submission: Local submission client behaved unexpectedly.">>"$failures_file"
fi
else
echo "job *NOT* submitted successfully!" 1>&2
echo "got error code from sbatch: $SLURM_RESULT !" 1>&2
echo "Submission: Local submission client failed.">>"$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_SCRIPT" "$LRMS_JOB_OUT" "$LRMS_JOB_ERR"
echo "----- exiting submit_slurm_job -----" 1>&2
echo "" 1>&2
exit 1
|