Software

Environment Modules

Most software on the HPC systems is managed by the LMod Environment Module system. Since there are many software packages available for use, and especially since there are a number of versions of some of these packages, it is not feasible to make all of the software accessible at once. With Environment Modules, it is easy to manage which version of each package that you want to use. Since software is added all the time, and since new versions are updated periodically, a complete list won't be given here, but some of them packages that are on the system are:

Anaconda Python, R, Matlab*, go, Gnu Compilers, Intel Compilers, Java

ANSYS*, NAMD, Gromacs, LAMMPS, VASP*, Abacus*, Gaussian*, OpenFOAM, Genoa, Genesis

Many Bioinformatics tools, Telemac, Tensorflow, PyTorch, Scuff-EM,

HDF, NetCDF, NCL, NCO, GDAL, Gizmo, Quantum-Espresso, Singularity

* indicates that this software is licensed to a specific group. Please check for availability.

To see exactly what is installed, and what versions of each package, run the command:

module avail

To see what modules you currently have loaded run:

module list

To search for modules use the "module spider program-name" command:

[blackbear@penobscot ~]$ module spider namd

Will return versions namd/2.9-gpu, namd/2.9, namd/2.11-gpu, namd/2.11

For detailed information about a specific module (including how to load the modules) use the module's full name. For example:

$ module spider namd/2.9-gpu

Once you have found a module that you would like to use, you can load it into your environment with the module load command. For instance:

module load namd/2.11-gpu