The Module System and What is Available

Owned by Simon Alexander, created
Last updated: Sep 30, 2024
6 min read

Goal: Introduce the LMOD Module System and the concept of dependencies.

What Have We Seen

Although on the login nodes we do have a gcc compiler and the Python language this only caters for a minority of users.

We can see that R is not available, nor most of the applications that researchers will require.

There are:

  • 10s of compilers and languages

  • 100s of applications and utilities.

  • 1000s of underlying libraries and commands.

We can not provide a system that provides everything all at once.

What we need is a method to enable users to find and select that they specifically need, and a method to allow them to configure and setup their sessions/environment to allow them to perform their analysis and research.

LMOD: An Environment Module System

What do we have available?

  • Compilers and eco systems: GNU family, Intel’s oneAPI, Nvidia’s hpc-sdk

  • Languages: C/C+, Fortran, Go, Java, Julia, Perl, Python, R, Ruby, Rust

  • Scientific libraries and toolkits: Built with a specific compiler: GNU by default

  • Standalone applications and utilities: Installed using:

    • Conda environments.

    • Containers: running Singularity (not Docker).

      • We can create a Singularity image from a Docker image.

    • Linux based Binaries/Executables

Check the MedicineBow Software Page.

What is Available?

What’s available: Using the Module System

# Modules currently loaded. []$ module list Currently Loaded Modules: 1) slurm/latest (S) 2) arcc/1.0 (S)
# What's available within my 'current' environment. # With respect to what modules I 'currently' have loaded. []$ module avail ...

What’s available? Compiler tree

[]$ module purge []$ module load gcc/14.2.0 []$ ml Currently Loaded Modules: 1) slurm/latest (S) 5) mpc/1.3.1_x86_64 2) arcc/1.0 (S) 6) zlib-ng/2.1.4_x86_64 3) gmp/6.2.1_x86_64 7) zstd/1.5.5_x86_64__programs_True 4) mpfr/4.2.0_x86_64 8) gcc/14.2.0

The gmp, mpc, mpfr, zlib-ng and zstd are know as dependencies.

Change Compiler

Purge Your Modules

Looking for Modules: module spider

Module load/spider: Dependencies

OpenMPI Tree: What Do You Notice?

What’s different between these command-lines?

What’s different between these command-lines? Dependencies

More module commands

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Your Basic Environment 

Workshop Home

Intro to using the Module System

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Setting Up Environments