Software
This page contains information about software on Midway. For more general information on how to run different types of jobs on Midway, consult Running Jobs.
RCC has a large selection of software available, but if you need software not currently available in the module system, send a detailed request to our Help Desk.
Using Software Modules
RCC uses Environment Modules for managing software. The modules system permits us to set up the shell environment to make running and compiling software easier. It also allows us to make available many software packages and libraries that would otherwise conflict with one another.
When you first log into Midway, you will be entered into a
basic user environment with minimal software available. The
module system is a script based system used to manage the user
environment and to “activate” software packages. In order to access
software that is installed on Midway, you must first load the
corresponding software module.
Basic module commands:
| Command | Description |
|---|---|
module avail |
lists all available software modules |
module avail [name] |
lists modules matching [name] |
module load [name] |
loads the named module |
module unload [name] |
unloads the named module |
module list |
lists the modules currently loaded for the user |
Module dependencies
Note that some modules require other specific modules, i.e., dependencies, to be loaded (or unloaded). If there is a conflict, you will need to explicitly unload the conflicting module (module unload ...), then load the desired module again. In certain cases, usually with loading an out-of-date module, you may get an error such as Error: Requirement... if a dependency is absent. In those situations, you can try module load -f <module> to force the module to load.
Commonly Used Applications
This guide contains instructions for some commonly used applications and environments including:
- Alphafold
- GROMACS
- LAMMPS
- MATLAB
- Mathematica
- NAMD
- Perl
- Python and Jupyter Notebook
- R
- Singularity
- Spark
- Stata
- Tensorflow and PyTorch
Note on software for AMD CPUs
For the amd partitions on Midway3, you need the software modules
that are built specifically for AMD CPUs.
module use /software/modulefiles-amd
module list
Full Software Module List
The best way to view the most current software offerings of RCC is to check the list of available software modules with the module avail command on Midway.