MEG analysis on Biowulf: Difference between revisions

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(Created page with "!!Under Construction!! ==== Biowulf brief intro ==== Biowulf (biowulf.nih.gov) is the head node of the Biowulf cluster at NIH - https://hpc.nih.gov/docs/userguide.html<br> He...")
 
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==== Making your own python module ====
==== Making your own python module ====
It is recommended to create an install script so that this can be sent to a slurm job
# echo mamba create -p ${PATH_TO_OUTPUT} condaPackage1 condaPackage2 conda-forge::condaForgePackage1 -y > installFile.sh
echo mamba create -p /data/ML_MEG/python_modules/mne0.24.1 jupyter ipython conda-forge::mne -y > python_install.sh
swarm -f ./python_install.sh -g 4 -t 4

Revision as of 11:41, 8 March 2022

!!Under Construction!!

Biowulf brief intro

Biowulf (biowulf.nih.gov) is the head node of the Biowulf cluster at NIH - https://hpc.nih.gov/docs/userguide.html
Helix - is the storage server attached to the biowulf cluster

Analysis of data should not be performed on the biowulf head node, but run through an sinteractive node or swarm process.
To start with, there are a limited number of commands loaded on the system. To access more programs use module load. To search, use module spider.

 e.g. module load afni


SAM MEG Data Analysis

 module load afni 
 module load ctf
 module load samsrcv3/20180713-c5e1042

MNE python data analysis

Making your own python module

It is recommended to create an install script so that this can be sent to a slurm job

 # echo mamba create -p ${PATH_TO_OUTPUT} condaPackage1 condaPackage2 conda-forge::condaForgePackage1  -y  > installFile.sh
 echo mamba create -p /data/ML_MEG/python_modules/mne0.24.1 jupyter ipython conda-forge::mne -y  > python_install.sh
 swarm -f ./python_install.sh -g 4 -t 4