Try using Princess to run notebook in Slurm

bin/slurm_calibrate.sh

@@ -45,8 +45,9 @@ then
 fi
 
 
-echo "Running script"
-${python_path} -m nbconvert --to rst --ExecutePreprocessor.timeout=36000 --ExecutePreprocessor.allow_errors=True --TemplateExporter.exclude_input=True --execute ${nb_path}
+echo "Running notebook"
+${python_path} -m princess ${nb_path} --save --on-error-resume-next
+${python_path} -m nbconvert --to rst --TemplateExporter.exclude_input=True ${nb_path}
 
 # stop the cluster if requested
 if [ "${ipcluster_profile}" != "NO_CLUSTER" ]

requirements.txt

@@ -24,10 +24,12 @@ jupyter-core == 4.6.1
 karabo_data == 0.7.0
 lxml == 4.5.0
 metadata_client == 3.0.5
+nbclient == 0.5.1
 nbconvert == 5.6.1
 nbformat == 5.0.7
 numpy == 1.19.1
 prettytable == 0.7.2
+princess == 0.1
 pypandoc == 1.4
 python-dateutil == 2.8.1
 pyyaml == 5.3