Software and Modules

Software packages on the cluster are managed through a modules environment system that handles PATH configuration and package-specific settings.

Module Commands

List Available Software

module avail

Load a Package

module load openmpi/2.1.2

View Package Details

module show openmpi/2.1.2
module whatis openmpi/2.1.2

Remove All Loaded Modules

module purge

Tip

Add module load commands to your ~/.bash_profile or ~/.bashrc for persistent loading.

Software Installation Options

Community Installation

Submit requests to the HPC team for widely-used packages: help-hpc@caltech.edu

Local/Group Installation

Users can compile software in home or group directories with custom build parameters.

Container Technology

Apptainer (formerly Singularity) is recommended for HPC workloads, offering MPI support and userspace operation. See Containers Guide.

Package Management

Spack

Unified software installation and module management tool.

Reference: https://spack.io/

Anaconda/Conda

Recommended for scientific Python environments.

Warning

Home directories have a 50 GB quota limit. Install Conda in your group directory instead.

Installation:

cd /resnick/groups/<groupname>/<username>
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh ./Miniconda3-latest-Linux-x86_64.sh

When prompted for installation location, use:

/resnick/groups/<groupname>/<username>/miniconda3

Create environments:

conda create -n myenv python=3.10
conda activate myenv

Share environments:

# Export
conda env export > environment.yml

# Import
conda env create -f environment.yml

Python Virtual Environments (venv)

Using the cluster’s Python module:

module load python3/3.8.5
python3 -m venv /path/to/environment
source /path/to/environment/bin/activate
pip install package_name