Questions about slurmUtils folder

[gao815]

Hello, expert
I was using this program for learning, and when I ran postMinimalPreprocessing, I found that the project did not provide a program for slurmUtils folder. I hope you can provide relevant procedures to facilitate learning and adaptation.

[mwcole]

Hello, SLURM is free software you can install yourself on a Linux server. It is standard on many compute clusters. More info here: https://slurm.schedmd.com/documentation.html

[gao815]

Sorry, I still don't get it. Is a file such as activity_noncircular_slurm.py in the code block for non-circular activation calculations also included in the slurm tool?

[gao815]

# this calculates fc for each task
from slurmUtils.py_to_slurm import *
file_name = 'FC'
py_file = 'fc_regression_slurm.py' # located in slurmUtils
for i in range(len(SUBJ_LIST)):
    py_to_slurm_singlesub(SUBJ_LIST[i],file_name,py_file,time = '00:5:00',suppress_output=False)

Can you provide a file like 'fc_regression_slurm.py， I can't figure out how it works

[mwcole]

The script uses SLURM commands via a Linux command line to request compute resources on a compute cluster. Once a compute node is obtained via SLURM, Python code is run on that node. Perhaps this overview would help: https://slurm.schedmd.com/overview.html

[gao815]

Ok, I roughly understand that slurm is a computer cluster tool. Do you still need to write such files as activity_noncircular_slurm.py? Could you please provide this file for easy study? Thank you！

[mwcole]

Luke was the one who wrote the code for this project, but I'm thinking his code was probably based on the Actflow Toolbox. Here is the function it was probably based on: https://github.com/ColeLab/ActflowToolbox/blob/master/connectivity_estimation/calcactivity_parcelwise_noncircular.py

[gao815]

Thank you for your answer. I tried to call this function before, and I used 718 parcels x conditions as the data size, but I found that it could not run. As for the data, should it be the data of the input voxels x conditions size as the input? What file is the data generally obtained from?

[gao815]

I hope you can provide relevant procedures to facilitate understanding and learning！

[mwcole]

It looks like you included both cortical and subcortical parcels in your data. If so, make sure the "cortexOnly" parameter is set to "False".