MEG Biowulf Setup - Revision history

Jstout: /* Edit .bashrc file in your home drive */

2025-09-24T20:17:25Z

Edit .bashrc file in your home drive

← Older revision		Revision as of 16:17, 24 September 2025
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	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

2025-01-24T21:48:23Z

← Older revision	Revision as of 17:48, 24 January 2025
(No difference)

2025-01-24T21:47:36Z

← Older revision		Revision as of 17:47, 24 January 2025
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	= Quick tutorial to generate most of the needed inputs for data analysis =

	== General Setup ==		== General Setup ==
	=== Mounting local computer to biowulf ===		=== Mounting local computer to biowulf ===
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	If editing your bashrc -- open two terminals in biowulf. '''If you misconfigure your .bashrc, you might 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 might 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 ===
			Aliases allow you to configure commands for easy use. <br>
			If you have a data directory that you use, you may want to add '''cddat="cd /data/MYDATADIR/blah/blah/data"'''
	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

2025-01-24T21:45:06Z

@@ Line 5: / Line 5: @@
   https://hpc.nih.gov/docs/hpcdrive.html
 == Configuring your bash shell environment ==
-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 might 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 ===
   umask 002   #Gives automatic group permissions to every file you create -- very very helpful for working with your team
@@ Line 16: / Line 16: @@
   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'
 === To Access Additional MEG modules ===
@@ Line 36: / Line 31: @@
 Add the following line to '''Use the following interpreter''': /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11 <br>
 [[File:Preferences panel spyder.png | 700px]] <br>

2025-01-24T21:40:59Z

Setting up spyder on biowulf

← Older revision		Revision as of 17:40, 24 January 2025
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	module load python/3.10		module load python/3.10
	spyder		spyder

			Click on the wrench icon <br>
	[[File:Spyder_config_button.png \| 700px]] <br><br>		[[File:Spyder_config_button.png \| 700px]] <br><br>
⚫	[[File:Preferences panel spyder.png \| 700px]] <br>

		⚫	Add the following line to '''Use the following interpreter''': /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11 <br>

		⚫	[[File:Preferences panel spyder.png \| 700px]] <br>
⚫	Add the following line to '''Use the following interpreter''': /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11

	== General Processing Pipeline ==		== General Processing Pipeline ==

2025-01-24T21:40:00Z

Setting up spyder on biowulf

← Older revision		Revision as of 17:40, 24 January 2025
Line 30:		Line 30:
	module load python/3.10		module load python/3.10
	spyder		spyder
			[[File:Spyder_config_button.png \| 700px]] <br><br>
		⚫	[[File:Preferences panel spyder.png \| 700px]] <br>

⚫	[[File:Preferences panel spyder.png \| 700px]]

		⚫	Add the following line to '''Use the following interpreter''': /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11

⚫	Add ~~this~~ ~~path~~ to the ~~python~~ ~~version~~: /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11

	== General Processing Pipeline ==		== General Processing Pipeline ==

2025-01-24T21:37:38Z

Setting up spyder on biowulf

← Older revision		Revision as of 17:37, 24 January 2025
Line 30:		Line 30:
	module load python/3.10		module load python/3.10
	spyder		spyder

			[[File:Preferences panel spyder.png \| 700px]]


	Add this path to the python version: /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11		Add this path to the python version: /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11

2025-01-24T21:27:14Z

Setting up spyder on biowulf

← Older revision		Revision as of 17:27, 24 January 2025
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	== Setting up spyder on biowulf ==		== Setting up spyder on biowulf ==
	module purge		module purge
	module load python		module load python/3.10
	spyder		spyder

	Add this path to the python version: /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11		Add this path to the python version: /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11



	== General Processing Pipeline ==		== General Processing Pipeline ==

2025-01-24T21:26:22Z

← Older revision		Revision as of 17:26, 24 January 2025
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	#Add the following line to your ${HOME}/.bashrc		#Add the following line to your ${HOME}/.bashrc
	module use --append /data/MEGmodules/modulefiles		module use --append /data/MEGmodules/modulefiles

			== Setting up spyder on biowulf ==
			module purge
			module load python
			spyder

			Add this path to the python version: /vf/users/MEGmodules/modules/mne1.5.1dev/bin/python3.11



	== General Processing Pipeline ==		== General Processing Pipeline ==

2024-02-13T21:40:22Z

@@ Line 1: / Line 1: @@
-# Quick tutorial to generate most of the needed inputs for data analysis
+= Quick tutorial to generate most of the needed inputs for data analysis =
-# Mounting local computer to biowulf
+=== Mounting local computer to biowulf ===
   https://hpc.nih.gov/docs/hpcdrive.html
 https://github.com/gjcooper/prespy