Available Software on Mercury
=============================

Booth IT maintains a curated set of software programs commonly in use by Booth researchers.
To facilitate setting up the computing environments, we use *software modules*.
Below are some examples of software modules that are currently available on Mercury:

* Python
* R
* Matlab
* Mathematica
* Stata

Once logged in to Mercury, modules can be used in the following manner.

* View the list of currently loaded modules: :code:`module list`
* View a list of the available software modules: :code:`module avail`
* Load a specific module: :code:`module load <module_name>` 
* Unload a specific module: :code:`module unload <module_name>`
* Unload *all* loaded modules: :code:`module purge`

.. note::
    To access modules commands, you must be logged in to a *compute* node

Loading and unloading modules is typically done for every session.
In addition, you may load modules inside a submission script.
More detailed information for the module command can be found by typing :code:`man module`.


.. code-block:: bash

    # make sure you are on a compute node
    $ srun --account=<accountname> --pty bash --login

    # list currently loaded modules
    $ module list
    No Modulefiles Currently Loaded.

    # check which version of R would be used
    $ which R
    /usr/bin/R

    # find out what modules are available
    $ module avail
    
    ------------------------- /apps/modulefiles ------------------------
    mpi/ompi/openmpi-x86_64
    python/booth/3.8
    R/3.6/3.6.2

    # now, load a specific version of R (R-3.6.2)
    $ module load  R/3.6/3.6.2

    # verify that the module has been loaded
    $ module list
    Currently Loaded Modulefiles:
      1) R/3.6/3.6.2

    # check the version of R    
    $ which R
    /apps/R-3.6.2/bin/R

    # unload all of the currently loaded modules
    $ module purge

    # check that the version of R has reverted    
    $ which R
    /usr/bin/R