Software stack
In Cecile softwares are provided systemwise through a so called software stack, a collection of softwares, which is generated using the Spack package manager.
A software stack contains a number of softwares necessary for your analysis and many more. If any software you might need is missing from the stack you need to contact cecile-admins-l at ovgu.de.
Type of stacks
Currently there are two kinds of stacks available:
- Current stack: A stack that is kept stable throughout one semester. Each semester a new stable stack is created from scratch, while the old
current stacksare still in place and can be used by specifying the the date in the following way:current_<date>. - Experimental stack: A flexible stack that is going to be frequently updated also upon user's request.
Multiple software versions in Experimental stack
Continuous updating in the experimental stack can lead to have multiple versions of the same software (e.g. python ~gcc@11.0 vs python ~gcc@11.1) in the experimental stack, therefore be careful to load the correct version when using the experimental stack. Usually back compatibility between software versions is mantained, but sometimes this might not be the case and some feature might have been changed.
Why two different stacks
If you need to use a software that is not yet available on Cecile (in the current stack), after your request, the missing software is going to be installed in the experimental stack
How to use the stacks
There are multiple ways to access the stack depending on the control you want over the versions of softwares you would like to use:
Load the Ipsy environment
Instead of loading every package individually, you can activate an evironment containing only the newest version of each package.
Loading environments takes time
Due to some changes in the package manager (Spack) currently loading an environment is a slow process that could take up to 5 minutes.
Now that the stack has been loaded, you can start each single software.
In order to see which softwares are available in the environment type the following command:
Via modules
For every installed package spack generates a module file in addition, this allows you to use the module command to load specific software.
Unlike the environment method, this method is extremely fast and it allows you to specify the version of the software you prefere.
Software names in the stack
Before loading a module it is advisable to check how the software you are interested in is named in the stack.
For example all python software are preceded by py-, thus to load pandas you need to type: module load py-pandas.
This naming convention is limited to stack, in your code software must have their usual names.
To see what packages are installed run
To load a package (in case a specific version is needed, load the version of the software shown by module avail)
Matlab software stack
The Matlab installation provided in the stack does include a variaty of toolboxes. In general we differentiate between toolboxes provided by MathWorks and third party toolboxes.
MathWorks toolboxes are toolboxes from https://www.mathworks.com/products.html like e.g. Image Processing Toolbox or Statistics and Machine Learning Toolbox and are included automatically.
Third party toolboxes like SPM or FieldTrip are also available in the central software stack but have to be loaded manually.
Don't use genpath to load all thirsparty toolboxes at once
Although matlab provides the possibility to load all toolboxes within a path by using genpath, this is not recommended to do because some of the toolboxes don't work well together and might break. For example spm will not start anymore.