Papermill Slurm Job Submission

Papermill Slurm Job Submission#

Author: Steffen Bollmann

Tools included in this workflow#

FSL

Dataset#

Please cite the database and dataset used in your example

Output CPU information#

!cat /proc/cpuinfo | grep 'vendor' | uniq
!cat /proc/cpuinfo | grep 'model name' | uniq

vendor_id	: AuthenticAMD
model name	: AMD EPYC 9454 48-Core Processor

Load software tools and import python libraries#

Please have a bloc for loading the different modules needed for your example. If you can not find all the required tools in Neurodesk, feel free to add tools using the web-based GUI https://www.neurodesk.org/neurocontainers-ui/

#load FSL 6.0.4
import module
await module.load('fsl/6.0.4')
await module.list()

['julia/1.10.4',
 'openssl/1.1',
 'python/3.10.4-gcccore-11.3.0',
 'libxslt/1.1.34-gcccore-11.3.0',
 'lxml/4.9.1-gcccore-11.3.0',
 'beautifulsoup/4.10.0-gcccore-11.3.0',
 'jupyter-server/1.21.0-gcccore-11.3.0',
 'jupyterlab/3.5.0-gcccore-11.3.0',
 'fsl/6.0.4']

Data preparation#

![ -f ./mp2rage-01.nii  ] && echo "$FILE exist." || wget https://imaging.org.au/uploads/Human7T/mp2rageModel_L13_work03-plus-hippocampus-7T-sym-norm-mincanon_v0.8.nii -O ./mp2rage-01.nii 
![ -f ./mp2rage-02.nii  ] && echo "$FILE exist." || cp ./mp2rage-01.nii ./mp2rage-02.nii 

 exist.
 exist.

Analysis#

subject_id='01'

import subprocess
result = subprocess.run(['bet', 'mp2rage-'+subject_id+'.nii', 
                        'mask-sub-'+subject_id+'.nii', '-R'], 
                       capture_output=True, text=True)

Running it on the HPC#

# Save Notebook and Run this on the terminal to test
# !papermill test-analysis.ipynb papermill_output.ipynb --parameters_raw subject_id 02

# create sbat file and make sure to replace account string and and execution times and modules loaded:
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