Hoffman2:Modules

Back to all things Hoffman2

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, FreeSurfer, FSL, ITKGray, ITK-SNAP, and MRIcron

Enabling the CCN Hoffman2 modules

1. SSH into Hoffman2
2. Use your favorite text editor (e.g. vim) to edit the file ~/.bash_profile

   • $ vim ~/.bash_profile

3. Insert these lines at the bottom of the file

   • Type G - (capital G) to go to the end of the file
   • Type A - (capital A) to go to the end of the line and enter insert mode
   • Type ENTER - to insert a newline
   • Type or paste in the lines below.

   • module use /u/project/CCN/apps/modulefiles
     umask 007

4. Save the file by typing

   • ESC + ":wq" + ENTER

5. Log out of Hoffman2 and the next time you log in, everything will be set for you to start working.

CCN Hoffman2 modules

AFNI

[AFNI https://afni.nimh.nih.gov/] (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.

Start an [interactive session https://www.hoffman2.idre.ucla.edu/computing/interactive-session/] on a compute node with qrsh. Then at the compute node shell prompt, enter:

module load afni

To run afni, enter:

afni