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Diffstat (limited to 'scripts/turbo-index-slurm')
-rwxr-xr-x | scripts/turbo-index-slurm | 85 |
1 files changed, 85 insertions, 0 deletions
diff --git a/scripts/turbo-index-slurm b/scripts/turbo-index-slurm new file mode 100755 index 00000000..a0f1bec5 --- /dev/null +++ b/scripts/turbo-index-slurm @@ -0,0 +1,85 @@ +#!/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 © 2016-2017 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/${RUN}-/"` + + echo "$NAME: $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 + echo "#SBATCH --nice=100" >> $SLURMFILE # Set priority very low to allow other jobs through + echo >> $SLURMFILE + + echo "#SBATCH --workdir $PWD" >> $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" + command="$command -j \`nproc\` -g $GEOM" + #command="$command --peaks=zaef" # Indexing parameters here + + echo $command >> $SLURMFILE + + sbatch $SLURMFILE + +done |