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#!/bin/sh
# Split a large indexing job into many small tasks and submit using SLURM
# ./turbo-index my-files.lst label my.geom /location/for/streams
# Copyright © 2016-2020 Deutsches Elektronen-Synchrotron DESY,
# a research centre of the Helmholtz Association.
#
# Authors:
# 2016 Steve Aplin <steve.aplin@desy.de>
# 2016-2017 Thomas White <taw@physics.org>
SPLIT=1000 # Size of job chunks
MAIL=you@example.org # Email address for SLURM notifications
INPUT=$1
RUN=$2
GEOM=$3
STREAMDIR=$4
# Set up environment here if necessary
#source /path/to/crystfel/setup.sh
# Generate event list from file above
list_events -i $INPUT -g $GEOM -o events-${RUN}.lst
if [ $? != 0 ]; then
echo "list_events failed"
exit 1
fi
# If you are using single-event files instead of multi-event ("CXI") ones,
# comment out the above lines and uncomment the following one:
#cp $INPUT events-${RUN}.lst
# Count total number of events
wc -l events-${RUN}.lst
# Split the events up, will create files with $SPLIT lines
split -a 3 -d -l $SPLIT events-${RUN}.lst split-events-${RUN}.lst
# Clean up
rm -f events-${RUN}.lst
# Loop over the event list files, and submit a batch job for each of them
for FILE in split-events-${RUN}.lst*; do
# Stream file is the output of crystfel
STREAM=`echo $FILE | sed -e "s/split-events-${RUN}.lst/${RUN}.stream/"`
# Job name
NAME=`echo $FILE | sed -e "s/split-events-${RUN}.lst/${RUN}-/"`
# Job number
NUMBER=${NAME##$RUN-}
POS=`expr $NUMBER \* $SPLIT + 1`
echo "$NAME (serial start $POS): $FILE ---> $STREAM"
SLURMFILE="${NAME}.sh"
echo "#!/bin/sh" > $SLURMFILE
echo >> $SLURMFILE
echo "#SBATCH --partition=mypartition" >> $SLURMFILE # Set your partition here
echo "#SBATCH --time=01:00:00" >> $SLURMFILE
echo "#SBATCH --nodes=1" >> $SLURMFILE
# It may be polite to set the priority very low to allow other jobs through:
#echo "#SBATCH --nice=100" >> $SLURMFILE
echo >> $SLURMFILE
echo "#SBATCH --job-name $NAME" >> $SLURMFILE
echo "#SBATCH --output $NAME-%N-%j.out" >> $SLURMFILE
echo "#SBATCH --error $NAME-%N-%j.err" >> $SLURMFILE
echo "#SBATCH --mail-type END" >> $SLURMFILE
echo "#SBATCH --mail-user $MAIL" >> $SLURMFILE
echo >> $SLURMFILE
echo "#source /path/to/crystfel/setup.sh" >> $SLURMFILE # Set up environment here (again) if necessary
echo >> $SLURMFILE
command="indexamajig -i $FILE -o $STREAMDIR/$STREAM --serial-start=$POS"
command="$command -j \`nproc\` -g $GEOM"
#command="$command --peaks=zaef" # Indexing parameters here
echo $command >> $SLURMFILE
sbatch $SLURMFILE
done
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