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Merged
m-reuter merged 4 commits into from
Jan 29, 2026
Merged

Internal benchmarking/execution time for segmentation pipeline #777

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a8a6224
Adds functionality to time the steps of the segmentation pipeline. Ti…
dkuegler Sep 24, 2024
d7029d4
Format run_fastsurfer commands
dkuegler Mar 10, 2025
3802dfd
make timeit automatic and remove all associated options from the run_…
dkuegler Jan 29, 2026
fedd39d
Add Pipeline and Module separation anchors for the execution time log
dkuegler Jan 29, 2026
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156 changes: 71 additions & 85 deletions recon_surf/fs_time
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Original file line number Diff line number Diff line change
@@ -1,27 +1,31 @@
#!/bin/bash
# fs_time

VERSION='$Id: fs_time,v 1.0 2024/03/08 15:12:00 kueglerd Exp $'
VERSION="\$Id: fs_time, v1.1 2024/11/13 15:04:00 kueglerd Exp \$"
outfile=""
key="@#@FSTIME "
flags=()
cmd=()
verbose=0
print_uptime=$FSTIME_LOAD

if [[ -z "$FSTIME_LOAD" ]]
if [[ -z "$print_uptime" ]]
then
# Turn on by default
export FSTIME_LOAD=1
print_uptime=1
fi

function usage()
{
cat << EOF

fs_time [options] command args
options:
-o outputfile : save resource info into outputfile
-k key
-l : report on load averages as from uptime
-o outputfile : save resource info into outputfile instead
-a : append to outputfile (see time)
-k key : key to find timing info in output
-l|--load : report on load averages as from uptime (default: \$FSTIME_LOAD or on)
--no-load : do not report on load averages
--debug : make output more verbose
EOF
}

Expand All @@ -44,31 +48,29 @@ Default fs_time Output (see also the manual page for /usr/bin/time):
2. Time stamp at the onset of execution
3. Command name
4. N Number of arguments passed to command
5. e Elapsed real time in seconds . This is the total
amount of time from when the command started to when it ended regardless
of how much of the CPU it got.
5. e Elapsed real time in seconds. This is the total amount of time from when the
command started to when it ended regardless of how much of the CPU it got.
6. S Total number of CPU-seconds that the process spent in kernel mode.
7. U Total number of CPU-seconds that the process spent in user mode.
8. P Percentage of the CPU that this job got, computed as (U+S)/e.
9. M Maximum resident set size of the process during its lifetime, in Kbytes.
10. F Number of major page faults that occurred while the process was running.
These are faults where the page has to be read in from disk.
11. R Number of minor, or recoverable, page faults. These are
faults for pages that are not valid but which have not yet been
claimed by other virtual pages. Thus the data in the page is
still valid but the system tables must be updated.
12. W Number of times the process was swapped out of main memory.
13. c Number of times the process was context-switched involuntarily
(because the time slice expired).
14. w Number of waits: times that the program was context-switched voluntarily,
for instance while waiting for an I/O operation to complete.
11. R Number of minor, or recoverable, page faults. These are faults for pages that
are not valid but which have not yet been claimed by other virtual pages. Thus
the data in the page is still valid but the system tables must be updated.
12. W Number of times the process was swapped out of main memory.
13. c Number of times the process was context-switched involuntarily (because the
time slice expired).
14. w Number of waits: times that the program was context-switched voluntarily, for
instance while waiting for an I/O operation to complete.
15. I Number of file system inputs by the process.
16. O Number of file system outputs by the process.
17. L L1 L5 L15 : load averages at 1, 5, and 15 min (with setenv FSTIME_LOAD 1)

Example:

fs_time -o resource.dat mri_convert orig.mgz myfile.mgz
fs_time mri_convert orig.mgz myfile.mgz
mri_convert orig.mgz myfile.mgz
reading from orig.mgz...
TR=2730.00, TE=3.44, TI=1000.00, flip angle=7.00
Expand All @@ -83,7 +85,7 @@ produces the information about resources. It also creates a file
resource.dat with the resource information. In this case, the above is
interpreted as:

@#@FSTIME : key for easy searching/grepping
@#@FSTIME : key for easy searching/grepping
mri_convert : command that was run
2016:01:21:18:27:08 : time stamp at the onset of execution year:month:day:hour:min:sec
N 2 : mri_convert was run with 2 arguments
Expand Down Expand Up @@ -112,87 +114,64 @@ EOF
function arg1err()
{
# param 1 : flag
echo "ERROR: flag $1 requires one argument"
echo "ERROR: Flag $1 requires one argument!"
exit 1
}

inputargs=("$@")
any_help=$(echo "$@" | grep -e -help)
if [[ -n "$any_help" ]]
then
usage
help
exit 0
fi
any_version=$(echo "$@" | grep -e -version)
if [[ -n "$any_version" ]]
then
echo "$VERSION"
exit 0
fi

# sourcing FreeSurfer should not be needed at this point,
# source $FREESURFER_HOME/sources.sh

cmdline=("$@")
while [[ $# != 0 ]]
do

flag=$1
flag="$1"
shift

case $flag in
-o)
if [[ "$#" -lt 1 ]] ; then arg1err "$flag"; fi
outfile=$1
shift
;;
-k)
if [[ "$#" -lt 1 ]] ; then arg1err "$flag" ; fi
key=$1
shift
;;
-l|-load)
export FSTIME_LOAD=1
;;
-no-load)
export FSTIME_LOAD=0
;;
-debug)
verbose=1
;;
*)
# must be at the start of the command to run
# put item back into the list
cmd=("$flag" "$@")
break
;;
-o|-k) if [[ "$#" -lt 1 ]] ; then arg1err "$flag"; fi ;;
esac

case "$flag" in
-help|--help) usage ; help ; exit 0 ;;
-version|--version) echo "$VERSION" ; exit 0 ;;
-o) outfile="$1" ; shift ;;
-k) key="$1" ; shift ;;
-a) flags+=("$flag") ;;
-l|-load|--load) print_uptime=1 ;;
-no-load|--no-load) print_uptime=0 ;;
-debug|--debug) verbose=1 ;;
# we must now be at the start of the command to run, so put all items back into the list
*) cmd=("$flag" "$@") ; break ;;
esac
done

if [[ "$verbose" == 1 ]]
then
echo "Parameters to fs_time:"
if [[ -n "$outfile" ]] ; then echo "-o $outfile" ; fi
if [[ "$key" != "@#@FSTIME " ]] ; then echo "-k $key" ; fi
echo "FSTIME_LOAD=$FSTIME_LOAD"
if [[ -n "$outfile" ]] ; then echo " -o $outfile" ; fi
if [[ "$key" != "@#@FSTIME " ]] ; then echo " -k $key" ; fi
if [[ "${#flags[@]}" -gt 0 ]] ; then echo " ${flags[*]}" ; fi
if [[ "$print_uptime" != "$FSTIME_LOAD" ]] && [[ -n "$FSTIME_LOAD" ]] ; then
if [[ "$print_uptime" == 1 ]] ; then echo " --load" ; else echo " --noload" ; fi
else
echo " FSTIME_LOAD=$FSTIME_LOAD" ;
fi
echo "command:"
echo "${cmd[*]}"
echo " ${cmd[*]}"
echo ""
fi

# CHECK PARAMS
if [[ "${#cmd[@]}" == 0 ]]
then
usage
echo "ERROR: no command passed to execute"
echo "ERROR: No command passed to execute!"
exit 1
fi

if [[ ! -e /usr/bin/time ]]
then
echo "ERROR: cannot find /usr/bin/time"
echo "ERROR: Cannot find /usr/bin/time!"
exit 1
fi

Expand All @@ -217,36 +196,43 @@ fi

nargs=$((${#cmd[@]} - 1 - npyargs))

function make_string ()
function make_uptime ()
{
# shellcheck disable=SC2207
uptime_data_array=($(uptime | sed 's/,/ /g'))
echo "L ${uptime_data_array[-3]} ${uptime_data_array[-2]} ${uptime_data_array[-1]}"
}

function make_fmt ()
{
# param 1 : key
# param 2 : command
# param 3 : num args
dt=$(date '+%Y:%m:%d:%H:%M:%S')
uptime_data_array=($(uptime | sed 's/,/ /g'))
echo "$1 $dt $2 N $3 ${uptime_data_array[-3]} ${uptime_data_array[-2]} ${uptime_data_array[-1]}"
export upt="L ${uptime_data_array[-3]} ${uptime_data_array[-2]} ${uptime_data_array[-1]}"
# param 4 : additional data
add=$4
if [[ "${#add}" -gt 0 ]] && [[ "${add:0:1}" != " " ]] ; then add=" $add" ; fi
echo "$1 $(date '+%Y:%m:%d:%H:%M:%S') $2 N $3$add"
}

if [[ "$FSTIME_LOAD" == 1 ]]
if [[ "$print_uptime" == 1 ]]
then
make_string "@#@FSLOADPRE" "$command" "$nargs"
uptime="$(make_uptime)"
make_fmt "@#@FSLOADPRE" "$command" "$nargs" "$uptime"
else
upt=""
uptime=""
fi

dt=$(date '+%Y:%m:%d:%H:%M:%S')
fmt="$key $dt $command N $nargs e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O $upt"
fmt="$(make_fmt "$key" "$command" "$nargs" "e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O$uptime")"

timecmd=("/usr/bin/time")
if [[ -n "$outfile" ]] ; then timecmd=("${timecmd[@]}" -o "$outfile"); fi
timecmd=("/usr/bin/time" "${flags[@]}")
if [[ -n "$outfile" ]] ; then timecmd+=(-o "$outfile"); fi
if [[ "$verbose" == 1 ]] ; then echo "${timecmd[@]}" -f "'$fmt'" "${cmd[@]}" ; fi
"${timecmd[@]}" -f "$fmt" "${cmd[@]}"
st=$?
if [[ -n "$outfile" ]] ; then cat $outfile; fi

if [[ "$FSTIME_LOAD" == 1 ]]
if [[ "$print_uptime" == 1 ]]
then
make_string "@#@FSLOADPOST" "$command" "$nargs"
make_fmt "@#@FSLOADPOST" "$command" "$nargs"
fi

exit $st
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