MEG analysis on Biowulf - Revision history

Jstout: /* To Access Additional MEG modules */

2025-09-24T20:26:12Z

To Access Additional MEG modules

← Older revision		Revision as of 16:26, 24 September 2025
Line 36:		Line 36:
	== MNE python data analysis ==		== MNE python data analysis ==
	===To Access Additional MEG modules===		===To Access Additional MEG modules===
	#Add the following line to your ${HOME}/.bashrc		#Add the following line to your ${HOME}/.bashrc -- if you haven't already done this in the paragraph or two above
	module use --append /data/MEGmodules/modulefiles		module use --append /data/MEGmodules/modulefiles

2025-09-24T20:25:27Z

Edit .bashrc file in your home drive

← Older revision		Revision as of 16:25, 24 September 2025
Line 21:		Line 21:
	umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team		umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team

	#Add modules ~~bin~~ path to access the MEG modules		#Add modules path to access the MEG modules
	~~PATH=~~/data/MEGmodules/~~bin:$PATH~~		module use --append /data/MEGmodules/modulefiles

	## Set up some aliases, so you don't have to type these out		## Set up some aliases, so you don't have to type these out
	alias sinteractive_small='sinteractive --mem=8G --cpus-per-task=4 --gres=lscratch:30'		alias sinteractive_small='sinteractive --mem=8G --cpus-per-task=4 --gres=lscratch:30'

2025-01-17T17:01:38Z

← Older revision		Revision as of 13:01, 17 January 2025
Line 28:		Line 28:
	alias sinteractive_medium='sinteractive --mem=16G --cpus-per-task=12 --gres=lscratch:100'		alias sinteractive_medium='sinteractive --mem=16G --cpus-per-task=12 --gres=lscratch:100'
	alias sinteractive_large='sinteractive --mem=24G --cpus-per-task=32 --gres=lscratch:150'		alias sinteractive_large='sinteractive --mem=24G --cpus-per-task=32 --gres=lscratch:150'

	=== Edit .bash_profile in your home drive ===
	#Set your default group (normally your default is your userID - which isn't helpful for your group
	#Type `groups` to see which groups you are part of
	newgrp <<YOUR GROUP ID>>



	== SAM MEG Data Analysis ==		== SAM MEG Data Analysis ==

2024-01-26T16:03:22Z

Edit .bashrc file in your home drive

← Older revision		Revision as of 12:03, 26 January 2024
Line 20:		Line 20:
	=== Edit .bashrc file in your home drive ===		=== Edit .bashrc file in your home drive ===
	umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team		umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team


	#Add modules bin path to access the MEG modules		#Add modules bin path to access the MEG modules
	PATH=/data/MEGmodules/bin:$PATH		PATH=/data/MEGmodules/bin:$PATH

2024-01-26T16:03:04Z

Edit .bashrc file in your home drive

← Older revision		Revision as of 12:03, 26 January 2024
Line 20:		Line 20:
	=== Edit .bashrc file in your home drive ===		=== Edit .bashrc file in your home drive ===
	umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team		umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team

			#Add modules bin path to access the MEG modules
			PATH=/data/MEGmodules/bin:$PATH

	## Set up some aliases, so you don't have to type these out		## Set up some aliases, so you don't have to type these out

2024-01-26T15:48:16Z

Edit .bashrc file in your home drive

← Older revision		Revision as of 11:48, 26 January 2024
Line 19:		Line 19:
	If editing your bashrc -- open two terminals in biowulf. If you misconfigure your .bashrc, you will not be able to log into biowulf. Having two terminals open allows you to fix anything that errors out.		If editing your bashrc -- open two terminals in biowulf. If you misconfigure your .bashrc, you will not be able to log into biowulf. Having two terminals open allows you to fix anything that errors out.
	=== Edit .bashrc file in your home drive ===		=== Edit .bashrc file in your home drive ===
	umask 002 #Gives automatic group permissions -- very very helpful for working with your team		umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team

	## Set up some aliases, so you don't have to type these out		## Set up some aliases, so you don't have to type these out

2024-01-26T15:47:40Z

@@ Line 15: / Line 15: @@
 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 ==

2022-05-10T17:11:46Z

Biowulf brief intro

← Older revision		Revision as of 13:11, 10 May 2022
Line 3:		Line 3:
	#For processing of data - reserve an sinteractive session		#For processing of data - reserve an sinteractive session
	sinteractive --mem=6G --cpus-per-task=4		sinteractive --mem=6G --cpus-per-task=4

	#Depending on your usage, you may need more --mem and more cpu cores. Also for jupyter notebook, you will need the --tunnel option		#Depending on your usage, you may need more --mem and more cpu cores. Also for jupyter notebook, you will need the --tunnel option
	Helix - is the storage server attached to the biowulf cluster. !!Do not upload/download data directly to biowulf - use helix!! <br>		Helix - is the storage server attached to the biowulf cluster. !!Do not upload/download data directly to biowulf - use helix!! <br>

2022-05-10T17:11:34Z

Biowulf brief intro

← Older revision		Revision as of 13:11, 10 May 2022
Line 2:		Line 2:
	Biowulf (biowulf.nih.gov) is the head node of the Biowulf cluster at NIH - https://hpc.nih.gov/docs/userguide.html<br>		Biowulf (biowulf.nih.gov) is the head node of the Biowulf cluster at NIH - https://hpc.nih.gov/docs/userguide.html<br>
	#For processing of data - reserve an sinteractive session		#For processing of data - reserve an sinteractive session
	sinteractive		sinteractive --mem=6G --cpus-per-task=4
			#Depending on your usage, you may need more --mem and more cpu cores. Also for jupyter notebook, you will need the --tunnel option
	Helix - is the storage server attached to the biowulf cluster. !!Do not upload/download data directly to biowulf - use helix!! <br>		Helix - is the storage server attached to the biowulf cluster. !!Do not upload/download data directly to biowulf - use helix!! <br>
	#Use scp for transfer or rsync -av (slower but some benefits)		#Use scp for transfer or rsync -av (slower but some benefits)

2022-05-03T16:17:33Z

Load Commandline MNE scripts for Processing Data

@@ Line 57: / Line 57: @@
                           already present. Defaults to os.environ['SUBJECTS_DIR'] if not
                           provided
 ==Best Practices for Group Data Preprocessing==