diff options
| -rw-r--r-- | Makefile.am | 4 | ||||
| -rw-r--r-- | scripts/turbo-index-lsf (renamed from scripts/turbo-index) | 5 | ||||
| -rwxr-xr-x | scripts/turbo-index-slurm | 85 |
3 files changed, 90 insertions, 4 deletions
diff --git a/Makefile.am b/Makefile.am index ba7078a1..49bb9fc8 100644 --- a/Makefile.am +++ b/Makefile.am @@ -181,9 +181,9 @@ script_DATA = scripts/alternate-stream scripts/cell-please \ scripts/find-pairs scripts/plot-cc-and-scale.R \ scripts/ave-resolution scripts/crystal-frame-number \ scripts/plot-radius-resolution \ - scripts/detector-shift scripts/turbo-index \ + scripts/detector-shift scripts/turbo-index-lsf \ scripts/gaincal-to-saturation-map scripts/move-entire-detector \ - scripts/split-by-mask + scripts/split-by-mask scripts/turbo-index-slurm EXTRA_DIST += $(script_DATA) diff --git a/scripts/turbo-index b/scripts/turbo-index-lsf index c11f521e..00e4ec15 100644 --- a/scripts/turbo-index +++ b/scripts/turbo-index-lsf @@ -3,9 +3,9 @@ RUN=$1 NOSAMPLE=`echo $RUN | sed -e 's/\-.*$//'` -GEOM=<name of geometry file> +GEOM=my.geom # Name of your geometry file -find <path to CXI files>/$RUN -name '*.cxi' > files-${RUN}.lst +find /path/to/CXI/files/$RUN -name '*.cxi' > files-${RUN}.lst # Set location of files list_events -i files-${RUN}.lst -g $GEOM -o events-${RUN}.lst wc -l events-${RUN}.lst rm -f split-events-${RUN}.lst files-${RUN}.lst @@ -18,6 +18,7 @@ for FILE in split-events-${RUN}.lst*; do NAME=`echo $FILE | sed -e "s/split-events-${RUN}.lst/${NOSAMPLE}-/"` echo "$NAME: $FILE ---> $STREAM" + # Set indexing parameters here bsub -q psanaq -o $NAME.log -J $NAME -n 12 -R "span[hosts=1]" \ indexamajig \ -i $FILE -o $STREAM -j 32 -g $GEOM --peaks=cxi 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 |