AFNI - Revision history

Mhanby@uab.edu at 19:46, 31 October 2016

2016-10-31T19:46:46Z

← Older revision		Revision as of 19:46, 31 October 2016
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	<pre>		<pre>
	$ mkdir -p ~~/scratch/user/USERNAME~~/jobs/afni		$ mkdir -p $USER_SCRATCH/jobs/afni
	$ cd ~~/scratch/user/USERNAME~~/jobs/afni		$ cd $USER_SCRATCH/jobs/afni
	</pre>		</pre>

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	Copy the dat directory "data" from the local host to a remote host's directory "afni"		Copy the dat directory "data" from the local host to a remote host's directory "afni"
	<pre>		<pre>
	$ scp -r data ~~USERNAME@~~cheaha.uabgrid.uab.edu:/scratch~~/user~~/USERNAME/jobs/afni		$ scp -r data cheaha.uabgrid.uab.edu:/data/scratch/USERNAME/jobs/afni
	</pre>		</pre>

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	4. cd to the data directory		4. cd to the data directory

	<pre> $ cd ~~/scratch/user/USERNAME~~/jobs/afni </pre>		<pre> $ cd $USER_SCRATCH/jobs/afni </pre>

	5. Run afni		5. Run afni

Tanthony@uab.edu: /* Run AFNI on Cheaha */ changed /lustre/scratch/ to /scratch/user/

2013-06-19T14:56:34Z

Run AFNI on Cheaha: changed /lustre/scratch/ to /scratch/user/

← Older revision		Revision as of 14:56, 19 June 2013
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	4. cd to the data directory		4. cd to the data directory

	<pre> $ cd /~~lustre~~/~~scratch~~/USERNAME/jobs/afni </pre>		<pre> $ cd /scratch/user/USERNAME/jobs/afni </pre>

	5. Run afni		5. Run afni

Tanthony@uab.edu: /* Copying AFNI data to Cheaha */ changed /lustre/scratch/ to /scratch/user/

2013-06-19T14:55:28Z

Copying AFNI data to Cheaha: changed /lustre/scratch/ to /scratch/user/

← Older revision		Revision as of 14:55, 19 June 2013
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	<pre>		<pre>
	$ mkdir -p /~~lustre~~/~~scratch~~/USERNAME/jobs/afni		$ mkdir -p /scratch/user/USERNAME/jobs/afni
	$ cd /~~lustre~~/~~scratch~~/USERNAME/jobs/afni		$ cd /scratch/user/USERNAME/jobs/afni
	</pre>		</pre>

Line 37:		Line 37:
	Copy the dat directory "data" from the local host to a remote host's directory "afni"		Copy the dat directory "data" from the local host to a remote host's directory "afni"
	<pre>		<pre>
	$ scp -r data USERNAME@cheaha.uabgrid.uab.edu:/~~lustre~~/~~scratch~~/USERNAME/jobs/afni		$ scp -r data USERNAME@cheaha.uabgrid.uab.edu:/scratch/user/USERNAME/jobs/afni
	</pre>		</pre>


	===Run AFNI on Cheaha===		===Run AFNI on Cheaha===

Tanthony@uab.edu at 14:55, 25 May 2012

2012-05-25T14:55:38Z

← Older revision		Revision as of 14:55, 25 May 2012
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	[http://afni.nimh.nih.gov/afni AFNI] (which might be an acronym for 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. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.		[http://afni.nimh.nih.gov/afni AFNI] (which might be an acronym for 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. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.

			AFNI installed on the Cheaha is ver AFNI_2011_12_21_1014
	AFNI installed on the Cheaha is ver AFNI_2011_12_21_1014.



	== AFNI on Cheaha ==		== AFNI on Cheaha ==
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			===Run AFNI on Cheaha===
	===Run AFNI ~~data~~ on Cheaha===


	1. ssh -X to Cheaha (from local machine)		1. ssh -X to Cheaha (from local machine)

Tanthony@uab.edu: /* AFNI Versions */

2012-05-24T17:26:54Z

AFNI Versions

← Older revision		Revision as of 17:26, 24 May 2012
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	$ module avail afni		$ module avail afni

	---------------------------------------------- /etc/modulefiles		---------------------------------------------- /etc/modulefiles -----------------------------------------------
	-----------------------------------------------
	afni/afni_linux		afni/afni_linux
	</pre>		</pre>

Tanthony@uab.edu: adde using on Cheaha

2012-05-24T17:18:53Z

adde using on Cheaha

← Older revision		Revision as of 17:18, 24 May 2012
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	== AFNI on ~~the Desktop~~ ==		== AFNI on Cheaha ==
			AFNI is pre-installed on the [[Cheaha]] research computing system. This allows users to run AFNI directly on the cluster without any need to install software.

	AFNI is an ~~X based program~~ that ~~can~~ be run on the Cheaha ~~cluster~~.		=== AFNI Versions ===
			Use the 'module' command to view a list of available AFNI versions. If the version that you require isn't listed, please open a help desk ticket to request the installation.

			The following is an example output of the command and doesn't necessarily represent the currently installed versions:
			<pre>
			$ module avail afni

			---------------------------------------------- /etc/modulefiles
			-----------------------------------------------
			afni/afni_linux
			</pre>

			=== Copying AFNI data to Cheaha===

			These instructions provide an example of how to create and submit a AFNI job on [[Cheaha]].

			First, create the working directory for the job- Replace 'USERNAME' with the account associated username on Cheaha.
			You can create any directory to run your job. It is recommended that the job directory be on the scratch (i.e. lustre filesystem) instead of the user home directory.

			<pre>
			$ mkdir -p /lustre/scratch/USERNAME/jobs/afni
			$ cd /lustre/scratch/USERNAME/jobs/afni
			</pre>

			Next, Copy all the files required for AFNI to the working directory.
			This has to done from the local machine.
			Eg.
			Copy the dat directory "data" from the local host to a remote host's directory "afni"
			<pre>
			$ scp -r data USERNAME@cheaha.uabgrid.uab.edu:/lustre/scratch/USERNAME/jobs/afni
			</pre>



			===Run AFNI data on Cheaha===


			1. ssh -X to Cheaha (from local machine)

			<pre> $ ssh -X USERNAME@cheaha.uabgrid.uab.edu </pre>

			At this point you are on the head node. Please do not run compute intensive jobs on the head node.

			2. Qlogin onto a compute node to run computation (on Cheaha terminal)

			<pre> $ qlogin -l vf=2G,h_rt=2:00:00</pre>

			You should be logged in to a compute node with memory requirement of 2G and run time of 2 hours. You can change the above requirements as needed.

			3. Load the AFNI module

			<pre> $ module load afni/afni_linux </pre>

			4. cd to the data directory

			<pre> $ cd /lustre/scratch/USERNAME/jobs/afni </pre>

			5. Run afni

			<pre> $ afni </pre>

			AFNI should launch as it does on the desktop.

Tanthony@uab.edu at 16:56, 24 May 2012

2012-05-24T16:56:30Z

← Older revision		Revision as of 16:56, 24 May 2012
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	[[http://afni.nimh.nih.gov/afni AFNI]] (which might be an acronym for 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. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.		[http://afni.nimh.nih.gov/afni AFNI] (which might be an acronym for 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. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.


			AFNI installed on the Cheaha is ver AFNI_2011_12_21_1014.



			== AFNI on the Desktop ==

			AFNI is an X based program that can be run on the Cheaha cluster.

Tanthony@uab.edu: started page

2012-05-24T16:44:56Z

started page

New page

{{Generic_stub}}

[[http://afni.nimh.nih.gov/afni AFNI]] (which might be an acronym for 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. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.