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Software and Environment Modules

All research software is pre-installed on a shared read-only tree at /opt/sw. You don't install it; you just load what you need with module.

module avail (below) is the live source of truth for what is installed and at which versions. If you need something that isn't there, or want details on license servers or known workarounds, ask Engineering IT.

The module command

Think of a module as an on-demand entry for a piece of software. Until you load it, it's not on your PATH; once loaded, its commands Just Work.

module avail                    # list everything installed
module avail matlab             # filter by name
module load matlab              # add MATLAB to your environment
matlab                          # now available
module unload matlab            # remove it
module list                     # what's currently loaded
module purge                    # unload everything

Some apps have multiple versions:

module avail abaqus
#   abaqus/2025 (default)   abaqus/2026
module load abaqus/2026       # load a specific version

If you just type module load abaqus you get the default (indicated by "(default)" in module avail).

Applications by category

These are pre-installed on all research compute nodes. Versions may change; check module avail for current state.

Engineering / CAE

Module Notes
matlab MATLAB R2025a. Includes Parallel Computing Toolbox for GPU. License: UMD site license.
abaqus 2025 default, 2026 available. Licensed via site FlexLM.
ansys 2026 R1 — Workbench, Fluent, Mechanical. Licensed via ENG research server.
comsol COMSOL Multiphysics 6.3. Licensed via ECE academic server.

Launch desktop apps from the Xfce menu (Applications → Education / Engineering) — they run the right module load automatically and start with GPU acceleration.

Neuroimaging

Module Notes
freesurfer FreeSurfer 8.2.0 — runs in a container. License auto-loaded.
fmriprep fmriprep 25.2.5 — runs in a container.
cpac C-PAC 1.8.7 — runs in a container.
fsl FSL 6.0.7.22. After module load fsl the GUI launcher is fsleyes; CLI tools (flirt, bet, fslmaths, ...) are on PATH as usual.
afni AFNI 26.1.00.
ants ANTs 2.6.5.
connectome-workbench 2.1.0.
c3d C3D nightly build.

Containerised tools (FreeSurfer, fmriprep, C-PAC) are transparent — after module load freesurfer, commands like recon-all and freeview work exactly as you'd expect. Bind mounts for your home dir, /mnt/lab-*, and /scratch are set up automatically.

Programming

Module Notes
miniconda3 conda + mamba for building your own Python environments. See python-and-conda.md.

Plus system compilers (gcc, g++, gfortran), make, Python, etc. are already on PATH — no module needed.

Desktop launchers

Inside a desktop session, your software is available three ways:

  • Research Software menu — top-left Xfce menu, Applications → Research Software. The maintained shortcut list, organised by category (Engineering, Neuroimaging, etc.).
  • Desktop icons — the most common tools have icons on the desktop itself for double-click launch.
  • Module load + run from a terminal — see the module quick reference below.

The Research Software menu and desktop icons currently include:

  • MATLAB
  • ANSYS Workbench / Fluent / Mechanical
  • COMSOL
  • Abaqus CAE (with 2025 and 2026 separately listed)
  • FreeSurfer / FreeView
  • FSLeyes (the FSL GUI; CLI tools are on PATH after module load fsl)
  • AFNI
  • Connectome Workbench

Each launcher uses a small wrapper called glrun that auto-detects whether the node has a GPU with hardware OpenGL: with a GPU it runs under vglrun for accelerated rendering, without one it runs the app directly on software OpenGL. You don't need to set LD_LIBRARY_PATH or call vglrun yourself.

Neurodesk menu (neuroimaging labs)

If you launched a Neurodesk Desktop tile, you'll also see a Neurodesk submenu under Applications, pre-built from the Neurodesk tool catalog. IT regenerates the menu after upstream catalog changes — it doesn't refresh by itself at session start. If a tool that's listed upstream is missing locally, email eit-help@umd.edu and we'll rebuild the menu. Treat the submenu as a preview: the long-term plan is to fold its most-used tools into the standard Research Software menu.

License servers

Most commercial software uses floating licenses from UMD-wide servers on campus. As long as you're on a UMD network (which you are, from the compute nodes) they just work.

Rare license failures are usually:

  • License server is temporarily unreachable — try again in a minute.
  • All concurrent seats are in use — try a different time of day, or talk to IT about who has licenses.

See the admin stack doc for exact license server details.

Requesting new software

Email Engineering IT at eit-help@umd.edu with:

  • Name and version of the software.
  • Where it's from (vendor URL, GitHub, PyPI, etc.).
  • Whether your lab has a license for it (for commercial tools).
  • Whether it should be installed as a module (most research tools) or into a container (complex pipelines with pinned dependencies).
  • How many people in your lab need it — one user is fine; whole-lab changes our priority.

For one-off scripts and niche Python packages, you probably want a conda env — python-and-conda.md covers that without needing IT.

"Can I install this myself?"

  • In your conda env: yes, freely.
  • Inside your lab share: yes — you can build any software into /mnt/lab-research/software/<name> and run it from there.
  • Into /opt/sw/: no — that's the shared read-only tree.
  • System-wide (apt, etc.): no — the node is managed by Puppet and any out-of-band install will be reverted on the next agent run.

module quick reference

module avail                    # everything
module avail <name>             # filter
module spider <name>            # find modules by keyword
module load <name>              # load default version
module load <name>/<version>    # load specific version
module unload <name>            # remove from env
module list                     # currently loaded
module purge                    # unload everything
module show <name>              # what does it set?
module help <name>              # app-specific notes