If you've read some of the documentation above (and if not, do so now!) then you'll know that command shells need to be told where to find files so they can run the commands that you type. All will know about standard system locations where programs from
geany are installed, but we don't install the science packages into those locations. So how does the shell find them?
In the background the shell maintains an environment variable called
PATH, which is a list of directories that it should search for files which match typed commands. To enable access to new programs we need to add the directory they're in to the
PATH. In the old days one would edit shell initialisation files to add items to the
PATH, but this is hard to manage and gets very complex if you have multiple packages which may bundle different, incompatible, versions of the same command.
To try to make life easier we're using Environment Modules - these are small scripts which abstract most of the setup details away, and allow packages to be added and removed from the shell as needed.
If you type
module avail you'll see a list of modules corresponding to the additional packages which are installed on the computer. One enables a package using
module load modulename and disables it using
module unload modulename. The modulefiles can set up chains of dependencies to ensure that all files you need for a complex package are available with a single command. This means much less editing of arcane shell configuration files, which is surely a good thing, though this may scare old-time users who have spent many years getting their config files to work!
For each of the science packages listed below we have an environment module available to enable it. If you want to have some of these enabled when you open a new shell then you can add a
module load line to your
Some of the purely graphical packages are also available via GNOME without loading a module.
To enable IDL type
load module idl - we only offer version 8.7 at this time so there is no need to specify the version number. With this module loaded you have access to the
idlde commands, and the
IDL_PATH (like the shell
PATH, only for IDL programs) is adjusted to include
~/idl and all subdirectories. Any IDL .pro files stored under
~/idl will be automatically available.
The module adjusts the
IDL_PATH variable to include access to useful IDL libraries. This module also automatically enables the base IDL module so simply running
module load idllibs will enable both IDL and these libraries.
This module enables access to the Solarsoft/SSWIDL environment. SSW requires tcsh to function, but rather than adjust the user shell we now run
sswidl via its own script. Running
module load ssw enables IDL, the third party libraries above, and Solarsoft. Type
ssw to start the SSWIDL environment.
module load procspec/base enables the basic plotting and analysis tools, along with IDL and the third-party libraries. A set of non-LTE model atmosphere analysis tools are also available and can be enabled via
module load procspec/nonlte. Simply typing
module load procspec will default to the base configuration.
mathematica command in the shell. If Mathematica is installed on the machine it is also available in GNOME without loading this module.
matlab command in the shell. If MATLAB is installed on the machine it is also available in GNOME without loading this module.
module load starlink enables the
starlink command which sets up additional paths and commands. Due to the age and complexity of the Starlink environment it has not been possible to configure it as a proper environment module, so even if the module is unloaded the changes to the environment will persist.
It would be very unwise to load this module into your shell by default.
gaia command from Starlink 2016A only - no other part of the Starlink software. This module can be unloaded properly as it's very simple.
aladin command which launches the Java-based desktop sky atlas client.
Two versions of this module exist.
module load ds9/7.6 provides the basic ds9 FITS viewer by typing
module load ds9/7.6-funtools loads ds9 and also adds the Funtools package to the system
PATH. If you simply run
load module ds9 then you default to the latter configuration.
To enable Funtools in ds9 you must select Analysis/Load Analysis Commands… and navigate to
/opt/funtools/bin/ where there is a
funtools.ds9 file - select this and the Funtools menu item will be added to the Analysis menu.
This module also loads the xpa module which is a protocol used to remote control DS9.
This module loads the MESA code itself and the MESA SDK (via the mesasdk module) which replaces the default compilers, etc, with versions known to work for MESA.
module load mesa will load the latest SDK (installed under
/opt/mesasdk) and set the
MESA_DIR variable to the mesa release installed under
topcat command which launches the TopCAT application.
For users who have an Anaconda Python install, running
module load miniconda3 will prepend the user Anaconda directory to the
PATH, so it becomes their default python. If you don't have an anaconda install in your home directory, or it's not in the default location, this will return an error.
This module enables use of OpenMPI libraries and commands.
imagej command in the shell. If ImageJ is installed on the machine it is also available in GNOME without loading this module.
pycharm.sh command in the shell. If PyCharm is installed on the computer it is also available in GNOME without loading this module.
clion.sh command in the shell. If CLion is installed on the computer it is also available in GNOME without loading this module.