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Commit 555b8396 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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RF: Remove old fsl_sub script - we can now use the new one from the fsl/fsl_sub project

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1 merge request!5RF: Remove old fsl_sub script - we can now use the new one from the fsl/fsl_sub project
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#!/bin/bash
# Copyright (C) 2007-2017 University of Oxford
# Authors: Dave Flitney, Stephen Smith, Matthew Webster and Duncan Mortimer
# SHCOPYRIGHT
export LC_ALL=C
###########################################################################
# Edit this file in order to setup FSL to use your local compute
# cluster.
###########################################################################
set +o errexit
###########################################################################
# The following section determines what to do when fsl_sub is called
# by an FSL program. If SGE_ROOT is set it will attempt to pass the
# commands onto the cluster, otherwise it will run the commands
# itself. There are two values for the METHOD variable, "SGE" and
# "NONE". Note that a user can unset SGE_ROOT if they don't want the
# cluster to be used.
###########################################################################
METHOD=SGE
unset module
if [[ "x$SGE_ROOT" = "x" ]] ; then
METHOD=NONE
else
QCONF=$(which qconf)
if [[ "x$QCONF" = "x" ]]; then
METHOD=NONE
echo "Warning: SGE_ROOT environment variable is set but Grid Engine software not found, will run locally" >&2
fi
fi
# stop submitted scripts from submitting jobs themselves
if [[ "X$FSLSUBALREADYRUN" = "Xtrue" ]] ; then
METHOD=NONE
echo "Warning: job on queue attempted to submit parallel jobs - running jobs serially instead" >&2
fi
if [[ "X$METHOD" = "XNONE" ]]; then
QCONF=echo
fi
FSLSUBALREADYRUN=true
export FSLSUBALREADYRUN
###########################################################################
# The following auto-decides what cluster queue to use. The calling
# FSL program will probably use the -T option when calling fsl_sub,
# which tells fsl_sub how long (in minutes) the process is expected to
# take (in the case of the -t option, how long each line in the
# supplied file is expected to take). You need to setup the following
# list to map ranges of timings into your cluster queues - it doesn't
# matter how many you setup, that's up to you.
###########################################################################
map_qname ()
{
if [[ "$1" -le 20 ]] ; then
queue=veryshort.q
elif [[ "$1" -le 120 ]] ; then
queue=short.q
elif [[ "$1" -le 1440 ]] ; then
queue=long.q
else
queue=verylong.q
fi
queueCmd=" -q $queue "
#echo "Estimated time was $1 mins: queue name is $queue"
}
###########################################################################
# Don't change the following (but keep scrolling down!)
###########################################################################
if [[ ! -z "${POSIXLY_CORRECT}" ]]; then
OLD_POSIXLY_CORRECT=${POSIXLY_CORRECT}
fi
POSIXLY_CORRECT=1
export POSIXLY_CORRECT
command=$(basename "$0")
usage ()
{
cat <<EOF
$command V1.1 - wrapper for job control system such as SGE
Usage: $command [options] <command>
$command gzip *.img *.hdr
$command -q short.q gzip *.img *.hdr
$command -a darwin regscript rawdata outputdir ...
-T <minutes> Estimated job length in minutes, used to auto-set queue name
-q <queuename> Possible values for <queuename> are "verylong.q", "long.q"
and "short.q". See below for details
Default is "long.q".
-a <arch-name> Architecture [e.g., darwin or lx24-amd64]
-p <job-priority> Lower priority [0:-1024] default = 0
-M <email-address> Who to email, default = $(whoami)@$(hostname -f | cut -d . -f 2-)
-j <jid> Place a hold on this task until job jid has completed
-t <filename> Specify a task file of commands to execute in parallel
-N <jobname> Specify jobname as it will appear on queue
-R <RAM> Max total RAM to use for job (integer in MB)
-l <logdirname> Where to output logfiles
-m <mailoptions> Change the SGE mail options, see qsub for details
-z <output> If <output> image or file already exists, do nothing and exit
-F Use flags embedded in scripts to set SGE queuing options
-s <pename>,<threads> Submit a multi-threaded task - requires a PE (<pename>) to be
configured for the requested queues.
<threads> specifies the number of threads to run
-v Verbose mode.
Queues:
There are several batch queues configured on the cluster, each with defined CPU
time limits. All queues, except bigmem.q, have a 8GB memory limit.
veryshort.q:This queue is for jobs which last under 30mins.
short.q: This queue is for jobs which last up to 4h.
long.q: This queue is for jobs which last less than 24h. Jobs run with a
nice value of 10.
verylong.q: This queue is for jobs which will take longer than 24h CPU time.
There is one slot per node, and jobs on this queue have a nice value
of 15.
bigmem.q: This queue is like the verylong.q but has no memory limits.
EOF
exit 1
}
nargs=$#
if [[ "$nargs" -eq 0 ]] ; then
usage
fi
#if the newer whitespace-safe getopt format is available, use it
if [[ $(getopt -T >/dev/null 2>&1; echo $?) == 4 ]]; then
eval set -- $(getopt -s bash T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
result=$?
else
set -- $(getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
result=$?
fi
if [[ "$result" != 0 ]] ; then
echo "What? Your arguments make no sense!"
fi
if [[ "$nargs" -eq 0 ]] || [[ $result != 0 ]] ; then
usage
fi
if [[ -z "${OLD_POSIXLY_CORRECT}" ]]; then
unset POSIXLY_CORRECT
else
POSIXLY_CORRECT=${OLD_POSIXLY_CORRECT}
export POSIXLY_CORRECT
fi
###########################################################################
# If you have a Parallel Environment configured for OpenMP tasks then
# the variable omp_pe should be set to the name you have defined for that
# PE. The script will work out which queues have that PE setup on them.
# Note, we support openmp tasks even when Grid Engine is not in use.
###########################################################################
omp_pe='openmp'
###########################################################################
# If you wish to disable processor affinities under Grid Engine then
# comment the following line.
# This instructs Grid Engine to bind the task to the number of job slots
# allocated to the job (or PE)
###########################################################################
proc_affinities="-binding linear:slots"
###########################################################################
# The following sets up the default queue name, which you may want to
# change. It also sets up the basic emailing control.
###########################################################################
queue=long.q
queueCmd=" -q long.q "
mailto=$(whoami)@$(hostname -f | cut -d . -f 2-)
MailOpts="a"
###########################################################################
# In the following, you might want to change the behaviour of some
# flags so that they prepare the right arguments for the actual
# cluster queue submission program, in our case "qsub".
#
# -a sets is the cluster submission flag for controlling the required
# hardware architecture (normally not set by the calling program)
#
# -p set the priority of the job - ignore this if your cluster
# environment doesn't have priority control in this way.
#
# -j tells the cluster not to start this job until cluster job ID $jid
# has completed. You will need this feature.
#
# -t will pass on to the cluster software the name of a text file
# containing a set of commands to run in parallel; one command per
# line.
#
# -N option determines what the command will be called when you list
# running processes.
#
# -l tells the cluster what to call the standard output and standard
# -error logfiles for the submitted program.
###########################################################################
if [[ -z "$FSLSUBVERBOSE" ]] ; then
verbose=0
else
verbose=$FSLSUBVERBOSE;
echo "METHOD=$METHOD : args=$*" >&2
fi
scriptmode=0
while [[ "$1" != -- ]] ; do
case "$1" in
-z)
if [[ -e "$2" || $("${FSLDIR}/bin/imtest" "$2") = 1 ]] ; then
exit 0
fi
shift;;
-T)
map_qname "$2"
shift;;
-q)
queue="$2"
queueCmd=" -q $queue "
"$QCONF" -sq "$queue" >/dev/null 2>&1
if [[ $? -eq 1 ]]; then
echo "Invalid queue specified!"
exit 127
fi
shift;;
-a)
acceptable_arch=no
available_archs=$(qhost | tail -n +4 | awk '{print $2}' | sort | uniq)
for a in $available_archs; do
if [[ "$2" = "$a" ]] ; then
acceptable_arch="yes"
fi
done
if [[ "$acceptable_arch" = "yes" ]]; then
sge_arch="-l arch=$2"
else
echo "Sorry arch of $2 is not supported on this SGE configuration!"
echo "Should be one of: $available_archs"
exit 127
fi
shift;;
-p)
# Not implmented
shift;;
-M)
mailto=$2
shift;;
-j)
jid=$2
sge_hold="-hold_jid $jid"
shift;;
-t)
taskfile=$2
if [[ -f "$taskfile" ]] ; then
tasks=$(wc -l "$taskfile" | awk '{print $1}')
if [[ "$tasks" -ne 0 ]]; then
sge_tasks="-t 1-$tasks"
else
echo "Task file ${taskfile} is empty"
echo "Should be a text file listing all the commands to run!"
exit -1
fi
else
echo "Task file (${taskfile}) does not exist"
exit -1
fi
shift;;
-N)
JobName=$2;
shift;;
-R)
RAM="-l mem_free=${2}M"
shift;;
-m)
MailOpts=$2;
shift;;
-l)
LogOpts="-o $2 -e $2";
LogDir="${2}/";
if [[ ! -e "${2}" ]]; then
mkdir -p "$2"
else
echo "${2}" | grep '/dev/null' >/dev/null 2>&1
if [[ $? -eq 1 ]] && [[ -f "${2}" ]]; then
echo "Log destination is a file (should be a folder)"
exit -1
fi
fi
shift;;
-F)
scriptmode=1;
;;
-v)
verbose=1
;;
-s)
pe_string=$2;
peName=$(echo "$pe_string" | cut -d',' -f 1)
peThreads=$(echo "$pe_string" | cut -d',' -f 2)
shift;;
esac
shift # next flag
done
shift
###########################################################################
# Don't change the following (but keep scrolling down!)
###########################################################################
commandline=("$@")
command="${commandline[0]}"
if [[ -z "$taskfile" ]] && [[ -z "$command" ]]; then
echo "Either supply a command to run or a parallel task file"
exit -1
fi
if [[ -z "$taskfile" ]] && [[ ! -x "$command" ]]; then
which "$command" >/dev/null 2>&1
if [[ $? -ne 0 ]]; then
echo "The command you have requested cannot be found or is not executable"
exit -1
fi
fi
if [[ "x$JobName" = x ]] ; then
if [[ "x$taskfile" != x ]] ; then
JobName=$(basename "$taskfile")
else
JobName=$(basename "$command")
fi
fi
if [[ -n "$tasks" ]] && [[ -n "${commandline[*]}" ]] ; then
echo "Spurious input after parsing command line: \"${commandline[*]}\"!"
echo "You appear to have specified both a task file and a command to run"
exit -1
fi
if [[ -n "$peName" ]]; then
# If the PE name is 'openmp' then limit the number of threads to those specified
if [[ "X$peName" = "X$omp_pe" ]]; then
OMP_NUM_THREADS=$peThreads
export OMP_NUM_THREADS
fi
fi
case "$METHOD" in
###########################################################################
# The following is the main call to the cluster, using the "qsub" SGE
# program. If $tasks has not been set then qsub is running a single
# command, otherwise qsub is processing a text file of parallel
# commands.
###########################################################################
SGE)
###########################################################################
# Test Parallel environment options
###########################################################################
if [[ -n "$peName" ]]; then
# Is this a configured PE?
"$QCONF" -sp "$peName" >/dev/null 2>&1
if [[ $? -eq 1 ]]; then
echo "${commandline[*]}"
echo "$peName is not a valid PE"
exit -1
fi
# Get a list of queues configured for this PE and confirm that the queue
# we have submitted to has that PE set up.
qstat -g c -pe "$peName" >/dev/null 2>&1
if [[ $? -eq 1 ]]; then
echo "No parallel environments configured!"
exit -1
fi
qstat -g c -pe "$peName" | sed '1,2d' | awk '{ print $1 }' | grep "^$queue" >/dev/null 2>&1
if [[ $? -eq 1 ]]; then
echo "${commandline[*]}"
echo "PE $peName is not configured on $queue"
exit -1
fi
# The -w e option will result in the job failing if there are insufficient slots
# on any of the cluster nodes
pe_options="-pe $peName $peThreads -w e"
fi
if [[ -z "$tasks" ]] ; then
if [[ "$scriptmode" -ne 1 ]] ; then
sge_command=(qsub -V -cwd -shell n -b y -r y $queueCmd $proc_affinities $pe_options -M $mailto -N "$JobName" -m $MailOpts $LogOpts $sge_arch $RAM $sge_hold)
else
sge_command=(qsub $proc_affinities $LogOpts $sge_arch $sge_hold)
fi
if [[ "$verbose" -eq 1 ]] ; then
echo "sge_command: ${sge_command[*]}" >&2
echo "executing: ${commandline[*]}" >&2
fi
exec "${sge_command[@]}" "${commandline[@]}" | awk '{print $3}'
else
sge_command=(qsub -V -cwd $queueCmd $proc_affinities $pe_options -M $mailto -N "$JobName" -m $MailOpts $LogOpts $sge_arch $RAM $sge_hold $sge_tasks)
if [[ "$verbose" -eq 1 ]] ; then
echo "sge_command: ${sge_command[*]}" >&2
echo "control file: $taskfile" >&2
fi
exec "${sge_command[@]}" <<EOF | awk '{print $3}' | awk -F. '{print $1}'
#!/bin/sh
#$ -S /bin/sh
command=\`sed -n -e "\${SGE_TASK_ID}p" $taskfile\`
exec /bin/sh -c "\$command"
EOF
fi
;;
###########################################################################
# Don't change the following - this runs the commands directly if a
# cluster is not being used.
###########################################################################
NONE)
if [[ "x$tasks" = "x" ]] ; then
if [[ "$verbose" -eq 1 ]] ; then
echo executing: "${commandline[*]}" >&2
fi
"${commandline[@]}" > "${LogDir}${JobName}.o$$" 2> "${LogDir}${JobName}.e$$"
ERR=$?
if [[ "$ERR" -ne 0 ]] ; then
cat "${LogDir}${JobName}.e$$" >&2
exit $ERR
fi
else
if [[ "$verbose" -eq 1 ]] ; then
echo "Running commands in: $taskfile" >&2
fi
n=1
while [[ "$n" -le "$tasks" ]] ; do
line=$(sed -n -e ''${n}'p' "$taskfile")
if [[ "$verbose" -eq 1 ]] ; then
echo "executing: $line" >&2
fi
/bin/sh <<EOF2 > "${LogDir}${JobName}.o$$.$n" 2> "${LogDir}${JobName}.e$$.$n"
$line
EOF2
n=$((n+1))
done
fi
echo $$
;;
esac
###########################################################################
# Done.
###########################################################################
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