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#!/bin/bash
#
# run RS notebook with specific data set.
#
#
# if we have gpus load cuda modules
if [ "$CUDA_VISIBLE_DEVICES" != "" ]
then
module load cuda11.3/toolkit
fi
module load Anaconda3/2021.11
#module load Singularity
#source /share/apps/rc/software/Anaconda3/2020.11/etc/profile.d/conda.sh
conda activate gpfs-policy
# active openmp if multiple CPUs
#export OMP_NUM_THREADS=${SLURM_NPROCS:-1}
#./watchme.sh ${SLURM_TASK_PID} &
#TAGNAME=slurm-${SLURM_JOBID}
# add tmp dir to path for singularity support
# this is where the interface to the kernel started in singularity is found
#PATH=$PATH:$TMPDIR
#echo $PATH
NB="$3"
jobid=${SLURM_ARRAY_JOB_ID:-$SLURM_JOB_ID}
papermillcmd="papermill \
-p dirname $1 \
-p glob_pattern $2 \
-k ${NBKERNEL:-base} \
${NB}.ipynb \
slurm-${jobid}_${SLURM_ARRAY_TASK_ID}_${NB}.ipynb"
echo $papermillcmd
$papermillcmd
pmreturn=$?
# make notebook read only after papermill to avoid corrupting experiment record
#chmod -w ${RESULTSDIR}${NB}_${CNAME}_${DATASET}_slurm-${SLURM_JOBID}.ipynb
if [ $pmreturn -ne 0 ]
then
echo "papermill failed"
exit 1
fi