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 (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 on a compute node with qrsh. Then at the compute node shell prompt, enter:

module load afni

To run afni, enter:

afni