Software

M3 gives users access to lots of different software.

How to use this section of the docs?

This page provides an overview of how software works on M3. In the left sidebar, you will see many pages:

• The first few pages are key topics that we think are most useful to our users.
• The remaining pages are an alphabetically sorted list of software available on M3. Click on one of these to understand how to access and use specific programs. This list may not be complete, please let us know if we are missing anything major!

How do we deliver software?

How is the software delivered?	Description	Examples
User-provided	We encourage users to manage their own software environments to maintain reproducible research and easily customise versions to fit your needs. We are happy to help if needed, and can install very common tools (such as Python or GCC) or assist with complex compilations (such as MPI tools).	Conda, Apptainer
System-installed	Some software is installed via the system package manager dnf. This software is immediately accessible to all users.	ncdu
Environment modules	Most software is installed in the form of environment modules. See Modules on M3.
Managed services	Very few programs are run as "managed services". This means the M3 admins maintain something like a server. Users generally need to request access to these.	CryoSPARC

Licensing and citing

Most software has some associated license and/or terms of use. If you use the software on M3, you are accepting those terms and agreeing to abide by them, including citing your usage of that software if needed. Some software is restricted and requires you to explicitly request access. If you cannot find the licensing terms and conditions, please contact our help desk.

Requesting new software to be installed

If you would like new software to be installed or upgraded, please contact our help desk with the following information:

• software
• version
• URL for download
• urgency
• if there are any licensing restrictions we need to impose