run-list-pickle-nb.sh

#!/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