turbo-index-lsf

#!/bin/sh

# Split a large indexing job into many small tasks and submit using LSF

# ./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

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

    # Set up environment here (again) if necessary
    echo "#source /path/to/crystfel/setup.sh" >> $SLURMFILE
    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
    # Note: if using --mille, each indexamajig job needs its own directory:
    # --mille-dir=mille-data-$NUMBER

    echo $command >> $SLURMFILE

    # Set your queue after "-q" below
    bsub -q myqueue -o $NAME.out -e $NAME.err -J $NAME -x sh $SLURMFILE

done