Hoffman2:Modules - Revision history

Hwang: /* Enabling the CCN Hoffman2 modules */

2021-05-06T17:06:00Z

Enabling the CCN Hoffman2 modules

← Older revision		Revision as of 17:06, 6 May 2021
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	# Run the following command to load the changes into your current environment		# Run the following command to load the changes into your current environment
	#:* <code>source ~/.bashrc</code>		#:* <code>source ~/.bashrc</code>
	# ~~Log~~ out of Hoffman2 and ~~the next time you~~ log in, ~~everything will~~ be ~~set for you~~ to ~~start working~~.		# Or log out of Hoffman2 and log in again, you should be able to use modules.

	==CCN Hoffman2 modules==		==CCN Hoffman2 modules==

Hwang: /* Enabling the CCN Hoffman2 modules */

2021-05-06T17:02:58Z

Enabling the CCN Hoffman2 modules

← Older revision		Revision as of 17:02, 6 May 2021
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	#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>umask 0022</pre>		#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>umask 0022</pre>
	# Save the file		# Save the file
	# Run the following command to ~~reload~~ the changes ~~you just made~~		# Run the following command to load the changes into your current environment
	#:* <code>source ~/.bashrc</code>		#:* <code>source ~/.bashrc</code>
	# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.		# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.

Hwang: /* Enabling the CCN Hoffman2 modules */

2021-05-06T17:01:25Z

Enabling the CCN Hoffman2 modules

← Older revision		Revision as of 17:01, 6 May 2021
Line 13:		Line 13:
	#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>umask 0022</pre>		#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>umask 0022</pre>
	# Save the file		# Save the file
			# Run the following command to reload the changes you just made
			#:* <code>source ~/.bashrc</code>
	# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.		# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.


	==CCN Hoffman2 modules==		==CCN Hoffman2 modules==

Hwang at 16:58, 6 May 2021

2021-05-06T16:58:52Z

← Older revision		Revision as of 16:58, 6 May 2021
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	# Insert these lines at the '''bottom''' of the file		# Insert these lines at the '''bottom''' of the file
	#:* <pre>module use /u/project/CCN/apps/modulefiles umask 007</pre>		#:* <pre>module use /u/project/CCN/apps/modulefiles umask 007</pre>
	~~# '''Important:''' remove or comment out these lines (if present):~~
	~~#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>source /u/project/FMRI/apps/etc/profile</pre>~~
	#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>umask 0022</pre>		#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>umask 0022</pre>
	# Save the file		# Save the file

Jpdiaz: added external links and fixed some basic errors

2020-03-22T20:53:31Z

added external links and fixed some basic errors

← Older revision		Revision as of 20:53, 22 March 2020
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	[[Hoffman2\|Back to all things Hoffman2]]		[[Hoffman2\|Back to all things Hoffman2]]

	[https://www.hoffman2.idre.ucla.edu/computing/modules/ Environmental Modules] ~~allow~~ users to dynamically modify their shell environment (e.g., $PATH, $LD_LIBRARY_PATH, etc.) in order to support a number of applications installed on the Hoffman2 Cluster. CCN supports several modules on Hoffman2 including: AFNI, ANTs, Caret,FSL, FreeSurfer, ITKGray, ITK-SNAP, and MRIcron.		[https://www.hoffman2.idre.ucla.edu/computing/modules/ Environmental Modules] allows users to dynamically modify their shell environment (e.g., $PATH, $LD_LIBRARY_PATH, etc.) in order to support a number of applications installed on the Hoffman2 Cluster. CCN supports several modules on Hoffman2 including: AFNI, ANTs, Caret, FSL, FreeSurfer, ITKGray, ITK-SNAP, and MRIcron.


	==Enabling the CCN Hoffman2 modules==		==Enabling the CCN Hoffman2 modules==

	# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]		# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]
	# Use <code>gedit</code> or your favorite [[Text Editors\|text editor]] (e.g. nano or vim) to edit the file <code>~/.bashrc</code>		# Use <code>gedit</code> or your favorite [[Text Editors\|text editor]] (e.g. nano or vim) to edit the file <code>~/.bashrc</code>
Line 14:		Line 16:
	# Save the file		# Save the file
	# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.		# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.


	==CCN Hoffman2 modules==		==CCN Hoffman2 modules==
	===AFNI===		===AFNI===

	[https://afni.nimh.nih.gov/ AFNI] (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.		[https://afni.nimh.nih.gov/ AFNI] (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.

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	===Caret===		===Caret===

	[http://brainvis.wustl.edu/wiki/index.php/Caret:About Caret] is a free, open-source, software package for ~~structuraland~~ functional analyses of the cerebral and cerebellar cortex.		[http://brainvis.wustl.edu/wiki/index.php/Caret:About Caret] is a free, open-source, software package for structural and functional analyses of the cerebral and cerebellar cortex.

	# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]		# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]
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	===DCMTK===		===DCMTK===

	[http://www.dcmtk.org/dcmtk.php.en DCMTK] is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.		[http://www.dcmtk.org/dcmtk.php.en DCMTK] is a collection of libraries and applications implementing large parts of the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.

	# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]		# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]
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	===FreeSurfer===		===FreeSurfer===

	[https://surfer.nmr.mgh.harvard.edu/ FreeSurfer] is an open source software suite for processing and analyzing (human) brain MRI images.		[https://surfer.nmr.mgh.harvard.edu/ FreeSurfer] is an open-source software suite for processing and analyzing (human) brain MRI images.

	# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]		# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]
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	===CCN Scripts===		===CCN Scripts===

	Load the ''ccnscripts'' module to run CCN-supported scripts on Hoffman2: setup_subject, [[Hoffman2:Scripts:setup_subject\|setup_subject]], [[Hoffman2:Scripts:fix_perms.sh\|fix_perms.sh]], etc.		Load the ''ccnscripts'' module to run CCN-supported scripts on Hoffman2: setup_subject, [[Hoffman2:Scripts:setup_subject\|setup_subject]], [[Hoffman2:Scripts:fix_perms.sh\|fix_perms.sh]], etc.
	# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]		# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]
	# Start an [https://www.hoffman2.idre.ucla.edu/computing/interactive-session/ interactive session] on a compute node with qrsh. Then at the compute node shell prompt, enter:		# Start an [https://www.hoffman2.idre.ucla.edu/computing/interactive-session/ interactive session] on a compute node with qrsh. Then at the compute node shell prompt, enter:
	#: <pre>module load ccnscripts</pre>		#: <pre>module load ccnscripts</pre>


			==External Links==

			*[http://modules.sourceforge.net/ Environment Modules]
			*[https://www.hoffman2.idre.ucla.edu/computing/modules/ Hoffman2 Computing Modules]
			*[https://www.hoffman2.idre.ucla.edu/software/ Hoffman2 Software]

Hwang: /* CCN Scripts */

2019-05-10T17:49:52Z

CCN Scripts

← Older revision		Revision as of 17:49, 10 May 2019
Line 135:		Line 135:

	===CCN Scripts===		===CCN Scripts===
	Load the ''ccnscripts'' module to run CCN-supported scripts on Hoffman2: setup_subject, :[[Hoffman2:Scripts:setup_subject\|setup_subject]], [[Hoffman2:Scripts:fix_perms.sh\|fix_perms.sh]], etc.		Load the ''ccnscripts'' module to run CCN-supported scripts on Hoffman2: setup_subject, [[Hoffman2:Scripts:setup_subject\|setup_subject]], [[Hoffman2:Scripts:fix_perms.sh\|fix_perms.sh]], etc.
	# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]		# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]
	# Start an [https://www.hoffman2.idre.ucla.edu/computing/interactive-session/ interactive session] on a compute node with qrsh. Then at the compute node shell prompt, enter:		# Start an [https://www.hoffman2.idre.ucla.edu/computing/interactive-session/ interactive session] on a compute node with qrsh. Then at the compute node shell prompt, enter:
	#: <pre>module load ccnscripts</pre>		#: <pre>module load ccnscripts</pre>

Hwang: /* CCN Scripts */

2019-05-10T17:49:40Z

CCN Scripts

← Older revision		Revision as of 17:49, 10 May 2019
Line 135:		Line 135:

	===CCN Scripts===		===CCN Scripts===
	Load the ''ccnscripts'' module to run CCN-supported scripts on Hoffman2: setup_subject, ~~setup_subject_2~~, [[Hoffman2:Scripts:fix_perms.sh\|fix_perms.sh]], etc.		Load the ''ccnscripts'' module to run CCN-supported scripts on Hoffman2: setup_subject, :[[Hoffman2:Scripts:setup_subject\|setup_subject]], [[Hoffman2:Scripts:fix_perms.sh\|fix_perms.sh]], etc.
	# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]		# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]
	# Start an [https://www.hoffman2.idre.ucla.edu/computing/interactive-session/ interactive session] on a compute node with qrsh. Then at the compute node shell prompt, enter:		# Start an [https://www.hoffman2.idre.ucla.edu/computing/interactive-session/ interactive session] on a compute node with qrsh. Then at the compute node shell prompt, enter:
	#: <pre>module load ccnscripts</pre>		#: <pre>module load ccnscripts</pre>

Dmargolis: /* Enabling the CCN Hoffman2 modules */

2018-03-02T23:18:29Z

Enabling the CCN Hoffman2 modules

← Older revision		Revision as of 23:18, 2 March 2018
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	# Insert these lines at the '''bottom''' of the file		# Insert these lines at the '''bottom''' of the file
	#:* <pre>module use /u/project/CCN/apps/modulefiles umask 007</pre>		#:* <pre>module use /u/project/CCN/apps/modulefiles umask 007</pre>
	# '''Important:''' remove or comment out ~~this line~~ (if present):		# '''Important:''' remove or comment out these lines (if present):
	#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>source /u/project/FMRI/apps/etc/profile</pre>		#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>source /u/project/FMRI/apps/etc/profile</pre>
			#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>umask 0022</pre>
	# Save the file		# Save the file
	# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.		# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.

Dmargolis at 22:16, 30 November 2017

2017-11-30T22:16:09Z

← Older revision		Revision as of 22:16, 30 November 2017
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	==Enabling the CCN Hoffman2 modules==		==Enabling the CCN Hoffman2 modules==
	# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]		# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]
	# Use your favorite [[Text Editors\|text editor]] (e.g. vim) to edit the file <code>~/.bashrc</code>		# Use <code>gedit</code> or your favorite [[Text Editors\|text editor]] (e.g. nano or vim) to edit the file <code>~/.bashrc</code>
	#:* <pre>$ ~~vim~~ ~/.bashrc</pre>		#:* <pre>$ gedit ~/.bashrc</pre>
	# Insert these lines at the '''bottom''' of the file		# Insert these lines at the '''bottom''' of the file
	~~#:* Type <code>G</code> - (capital G) to go to the end of the file~~
	~~#:* Type <code>A</code> - (capital A) to go to the end of the line and enter insert mode~~
	~~#:* Type <code>ENTER</code> - to insert a newline~~
	~~#:* Type or paste in the lines below.~~
	#:* <pre>module use /u/project/CCN/apps/modulefiles umask 007</pre>		#:* <pre>module use /u/project/CCN/apps/modulefiles umask 007</pre>
	# '''Important:''' remove or comment out this line (if present):		# '''Important:''' remove or comment out this line (if present):
	#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>source /u/project/FMRI/apps/etc/profile</pre>		#:* <pre><nowiki>#</nowiki> Remove or comment out this line! <nowiki>#</nowiki>source /u/project/FMRI/apps/etc/profile</pre>
	# Save the file ~~by typing~~		# Save the file
	~~#:* <code>ESC + ":wq" + ENTER</code>~~
	# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.		# Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.

Dmargolis at 20:48, 7 November 2017

2017-11-07T20:48:34Z

← Older revision		Revision as of 20:48, 7 November 2017
Line 5:		Line 5:
	==Enabling the CCN Hoffman2 modules==		==Enabling the CCN Hoffman2 modules==
	# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]		# [[Hoffman2:Accessing the Cluster#SSH - Command Line\|SSH into Hoffman2]]
	# Use your favorite [[Text Editors\|text editor]] (e.g. vim) to edit the file <code>~/.~~bash_profile~~</code>		# Use your favorite [[Text Editors\|text editor]] (e.g. vim) to edit the file <code>~/.bashrc</code>
	#:* <pre>$ vim ~/.~~bash_profile~~</pre>		#:* <pre>$ vim ~/.bashrc</pre>
	# Insert these lines at the '''bottom''' of the file		# Insert these lines at the '''bottom''' of the file
	#:* Type <code>G</code> - (capital G) to go to the end of the file		#:* Type <code>G</code> - (capital G) to go to the end of the file