Software

Software Stack

To make all software needed by the users available in a reproducable way Medusa uses software stacks.

Further information can be found via Software stack

AFNI

AFNI ships with commands which are named the same as commands from other packages, so to enable AFNI, run the following:

source /etc/afni/afni.sh

This needs to be run each time you start a new session on the cluster. If you prefer that it be run automatically, you can add it to your .zshrc file.

NOTE: The following commands are known to have conflicts: whirlgif (FSL, wims), gifti_test (FreeSurfer), gifti_tool (FreeSurfer), nifti1_test (Niftilib), nifti_stats (Niftilib), nifti_tool (Niftilib), and whereami (whereami).

ANTs

ANTs' configuration is setup using something called "environmental modules."

First, "modules" must be loaded:

source /etc/profile.d/modules.sh

Then, to load version 2.2.0, run the following:

module load ants/2.2.0

Now you can use ANTs.

The process needs to be performed each time you start a new session on the cluster. If you'd rather it be done automatically, add the following lines to your .zshrc file.

source /etc/profile.d/modules.sh
module load ants/2.2.0

NOTE: There are no known namespace conflicts with other commands, so it should be safe to add the above lines to your .zshrc.

FreeSurfer

FreeSurfer's configuration is setup using something called "environmental modules."

First, "modules" must be loaded:

source /etc/profile.d/modules.sh

Then, you can query which versions of FreeSurfer are available:

module avail freesurfer

Then, to load version 6.0, run the following:

module load freesurfer/6.0

Now you can use FreeSurfer.

The process needs to be performed each time you start a new session on the cluster. If you'd rather it be done automatically, add the following lines to your .zshrc file.

source /etc/profile.d/modules.sh
module load freesurfer/6.0

NOTE: The following commands are known to have conflicts: gifti_test (AFNI), gifti_tool (AFNI), and dsh (dsh).

FSL

FSL ships with commands which are named the same as commands from other packages, so all FSL commands are prepended with fsl5.0-.

To configure FSL with defaults and remove the fsl5.0- prefix, run the following:

source /etc/fsl/fsl.sh

This needs to be run each time you start a new session on the cluster. If you prefer that it be run automatically, you can add it to your .zshrc file.

NOTE: The following commands are known to have conflicts: whirlgif (AFNI) and cluster (graphviz).

MATLAB

Multiple versions of Matlab are installed on the cluster. Because of this, there is no single matlab command. Instead, each version is suffixed with its version number (for example matlab94).

This suffixing is also applied to mex, mbuild, lmutil, and mcc.

You can check the current license usage by running:

lmutil96 lmstat -a -c 1984@liclux.urz.uni-magdeburg.de

Python

Python 2.7 and 3.5 are installed on the cluster — along with a wide variety of modules that are available to import.

If you need a python module that is not yet installed and think it is of interest and utility to other cluster users, just ask Alex to deploy it on the cluster. Alternatively, you can install it in a virtualenv.

R

R 3.3 is installed on the cluster — along with a wide variety of packages from CRAN that are available via the library() command.

If you need an R package that is not yet installed (and there is a Debian package for it), just ask Alex to deploy it on the cluster. Alternatively, you can install it from CRAN.