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Managing Software on the Turing Cluster

TLDR

To load software on turing, use the module system. The command module avail <name> will search, and module load <name> will load it in to you environment.

You Can't Install Your Own Software

On the Turing cluster, users are not permitted to install software system-wide. This is to ensure:

  • 🔒 Security: Prevent unauthorized or harmful software from affecting the cluster.
  • ⚙️ Stability: Maintain a consistent environment for all users.
  • 📈 Performance: Avoid conflicts between different software versions.

But don't worry! There are ways to use the software you need.

Using the Module System

The cluster uses a module system to manage software. Modules allow you to load and unload different software packages easily within your session or job submission scripts.

Listing Available Modules

To search avaialable modules use:

module avail <name> #(e.g., `module avail python`).

This will display a list of software packages you can use.

Tip

To display all avaialable modules use module avail with no name. This list is very long.

Loading Modules

To load a module on the Turing cluster, use the module load command followed by the module name. For example:

module load python/3.8.13

This adds the software and its dependencies to your environment, allowing you to use it in your session.

Key Commands for Managing Modules

  • Load a module: module load <module_name>
  • Check loaded modules: module list
  • Unload a module: module unload <module_name>

Always ensure you load the correct versions of modules required for your workflow, as conflicting versions may lead to errors. Modules are session-specific. You must reload them in every new session unless added to your initialization file .bashrc.

Login and Compute nodes

Any modules loaded on the login node will be loaded when running a job on a compute node.

Loading Modules in SLURM Job Scripts

To use a software package during a SLURM job, it is best to load modules directly within your job submission script.

Here’s an example of how to structure a submission script to load commonly used software modules:

#!/bin/bash
#SBATCH --job-name=my_job
#SBATCH --time=01:00:00
#SBATCH --mem=4G

# Load the necessary modules
module load gcc/12.1.0/
module load python/3.8.13/

# Run your application
python my_script.py

By including module load commands in your script, the environment will be set up for the job, ensuring the required software is available.

You can verify loaded modules with:

module list

And unload them when no longer needed:

module unload <module_name>