Software on Atlas

LMOD

  • Installed software on Atlas can be accessed via LMOD.
    • Allows a single system to accommodate multiple versions of the same software
    • Good for reproducibility - specified version of software is used in re-runs of analysis, preventing changes due to version updates
    • Users can select the version they want
  • Example commands
    • module list / ml list
    • module avail / ml avail
    • module load <software> / ml load <software>
    • module unload <software> / ml unload <software>
    • module swap <software/1.1> <software/2.1> / ml swap <software/1.1> <software/2.1>

Containers

Some software on Atlas is available via containers.

  • Standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another
  • Helps users avoid installation issues
    • Dependency difficulties
    • Compilation problems
    • Permission issues
    • Compatibility issues
  • Singularity
    • ml singularity
    • ml avail shows software available via containers only when singularity is loaded