From 1bb8547c305ffefa0db417eea9e2def91fe0c7e9 Mon Sep 17 00:00:00 2001
From: John-Paul Robinson <jpr@uab.edu>
Date: Fri, 30 Jun 2023 12:59:40 -0500
Subject: [PATCH] Add papermill job wrapper script to run pickling notebook

---
 run-list-pickle-nb.sh | 53 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100755 run-list-pickle-nb.sh

diff --git a/run-list-pickle-nb.sh b/run-list-pickle-nb.sh
new file mode 100755
index 0000000..3ae2867
--- /dev/null
+++ b/run-list-pickle-nb.sh
@@ -0,0 +1,53 @@
+#!/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
+
-- 
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