diff --git a/doc/scripts/bin_dssc_module_job.sh b/doc/scripts/bin_dssc_module_job.sh index 247cfe67d304cae6a02eb4f0f7f74eff5c4e566f..2f3dfb246e98b31ddb85a729fea9710ab1be5bba 100644 --- a/doc/scripts/bin_dssc_module_job.sh +++ b/doc/scripts/bin_dssc_module_job.sh @@ -5,21 +5,49 @@ #SBATCH --mail-type=END,FAIL #SBATCH --output=logs/%j-%x.out -PROPOSAL=2719 -DARK=$1 -RUN=$2 -MODULE_GROUP=$3 +while getopts ":p:d:r:k:g:t:s:m:" option +do + case $option in + p) PROPOSAL="$OPTARG";; + d) DARK="$OPTARG";; + r) RUN="$OPTARG";; + k) KERNEL="$OPTARG";; + m) MODULE_GROUP="$OPTARG";; + x) XAXIS="$OPTARG";; + b) BINWIDTH="$OPTARG";; + \?) echo "Unknown option" + exit 1;; + :) echo "Missing option for input flag" + exit 1;; + esac +done +# Load xfel environment source /etc/profile.d/modules.sh module load exfel module load exfel_anaconda3/1.1 echo processing run $RUN -OUTPATH=/gpfs/exfel/exp/SCS/202002/p002719/scratch/tests -mkdir $OUTPATH/r$RUN +PDIR=$(find-proposal $PROPOSAL) +PPROPOSAL="p$(printf '%06d' $PROPOSAL)" +RDIR="$PDIR/usr/processed_runs/r$(printf '%04d' $RUN)" +mkdir $RDIR -# Run papermill -python3 -c "import papermill as pm; pm.execute_notebook('Dask DSSC module binning.ipynb', \ -'$OUTPATH/r$RUN/output$MODULE_GROUP.ipynb', \ -parameters=dict(proposalNB='$PROPOSAL', dark_runNB='$DARK', runNB='$RUN', module_group='$MODULE_GROUP', \ -path='$OUTPATH/r$RUN/', kernel='xfel'))" +NB='Dask DSSC module binning.ipynb' + +# kernel list can be seen from 'jupyter kernelspec list' +if [ -z "${KERNEL}" ]; then + KERNEL="toolbox_$PPROPOSAL" +fi + +python -c "import papermill as pm; pm.execute_notebook(\ + '$NB', \ + '$RDIR/output$MODULE_GROUP.ipynb', \ + kernel_name='$KERNEL', \ + parameters=dict(proposalNB=int('$PROPOSAL'), \ + dark_runNB=int('$DARK'), \ + runNB=int('$RUN'), \ + module_group=int('$MODULE_GROUP'), \ + path='$RDIR', \ + xaxis='$XAXIS', \ + bin_width=float('$BINWIDTH')))" diff --git a/doc/scripts/boz_parameters_job.sh b/doc/scripts/boz_parameters_job.sh index 99a4b121b23537ec1e98a069d342f6033ba34249..100b713d415c65112bccf7dd4d35ff8f140eead3 100644 --- a/doc/scripts/boz_parameters_job.sh +++ b/doc/scripts/boz_parameters_job.sh @@ -27,8 +27,6 @@ do esac done -echo ${KERNEL} - # Load xfel environment source /etc/profile.d/modules.sh module load exfel