Using the supported software via modules

Running a software or application in Linux requires certain changes on the environment variables. Some variables are common (such as $PATH, $LD_LIBRARY_PATH), some are application specific (such as $R_LIBS for R, $SUBJECTS_DIR for Freesurfer.)

In order to help configure the shell environment for running the supported software, a tool called Environment Modules is used in the cluster. Hereafter, we introduce few mostly used module commands for using the supported software in the cluster.

Note

You should have the module command available if you login to one of the mentat access node using a SSH client (e.g. putty). In the virtual terminal (i.e. GNOME Terminal or Konsole) of a VNC session, the module command may not be available immediately. If it happens to you, make sure the following lines are presented in the ~/.bashrc file.

if [ -f /etc/bashrc ]; then
    source /etc/bashrc
fi

For example, run the following command in a terminal:

$ echo 'if [ -f /etc/bashrc ]; then source /etc/bashrc; fi' >> ~/.bashrc

Please note that you should close all existing terminals in the VNC session and start from a new terminal. In the new terminal, you should have the module command available.

Showing available software

Firstly, one uses the module command to list the supported software in the cluster. This is done by the following command:

$ module avail
----------------------------- /opt/_modules --------------------------------------------
32bit/brainvoyagerqx/1.10.4   cluster/1.0(default)   matlab/7.0.4    mcr/R2011b
32bit/brainvoyagerqx/1.3.8    cuda/5.0               matlab/7.1.0    mcr/R2012a
32bit/brainvoyagerqx/1.8.6    cuda/5.5(default)      matlab/R2006a   mcr/R2012b(default)
32bit/ctf/4.16                dcmtk/3.6.0(default)   matlab/R2006b   mcr/R2013a
32bit/mricro/1.38_6           fsl/5.0.6              matlab/R2014a   python/2.6.5

## ... skip ...

As shown above, the software are represented as modules organised in name and version. From the list, one selects a software (and version) by picking up a corresponding module. Assuming that we are going to run FSL version 5.0.6, the module to chose is named as fsl/5.0.6.

Tip: Software are installed in a directory with respect to the hierachy of the module names. For instance, the FSL software corresponding to the module fsl/5.0.6 is installed under the directory /opt/fsl/5.0.6.

Loading software

After chosing a module, the next step is to load it to configure the shell environment accordingly for running the software. This is done via the load command. For example, to configure fsl/5.0.6 one does

$ module load fsl/5.0.6

After that, one can check if a right version of the FSL executable is available. For example,

$ which fsl
/opt/fsl/5.0.6/bin/fsl

Tip

You can load more than one module at the same time.

Unloading software

When a loaded software is no longer needed, one can easily rollback the shell environment configuration by unloading the specific module. For instance,

$ module unload fsl/5.0.6

As the configuration for running FSL version 5.0.6 is removed, the FSL executable becomes unavailable. It makes sure that the environment is clean for running other software.

Listing loaded software

In most of cases, you will load several software in one shell environment. To get an overview on the software loaded in the current shell, one can use the list option. For example,

% module list
Currently Loaded Modulefiles:
1) fsl/5.0.6       2) R/3.1.2         3) cluster/1.0     4) matlab/R2012b

Pre-loaded software

Right after logging into the cluster, you will find several pre-loaded software. You can find them via module list command. Although you are free to unload them using the module unload command, you should always keep the module cluster/1.0 loaded as it includes essential configurations for running computations in the cluster.

Tip

You should always keep the cluster/1.0 module loaded.