Software environment

General usage apps

In general, software is installed in the master node of marbits by the system administrators. Different versions of the same software can co-exist in the cluster, as they have to be explicitly loaded using modules. Such modules have been crafted so as they include all the dependencies that the program may have and allow you to select different versions, for reproducibility or compatibility with other programs. To see what software is available at marbits do

module avail

Loading (and unloading) apps.

To load a particular version of a program you have to do it as follows:

module load program_name/version

The executables and man pages for the software should be in your $PATH, so you can call them without having to specify any route.

To see what modules are currently loaded do

module list

Make sure that your sbatch script loads all the modules needed after the header (see examples on how to run jobs).

If you want to unload a module, just do

module unload 

or unload all modules at once

module purge

Getting help

The following commands will give you information on the specifics of each app such as the program name, version, URL or particular instructions if needed. Please type:

module help program_name/version

or

module whatis program_name/version

Specific software

If you need a particular (and sensible) piece of software, you can install it in your home (remember that you have a 5 GB quota!) and run it from there, or ask the system administrator to install it and build a module for you. This doesn’t apply to your home-made scripts…