Research Computing and HPC

A starting page for research computing and HPC. Contains links to all of the related knowledge-base articles.

Below is a list of articles sorted by various topics in relation to research computing and HPC clusters.

Overview

Introduction to HPC clusters

• What is an HPC Cluster
• Matilda HPC Cluster
• Matilda HPC Cluster Rates 2025-FY26
• Matilda HPC Cluster Rates 2022-2024
• Matilda Rate FAQ
• HPC Training Workshops

Using the Cluster

• Requesting a Matilda Account
• Logging into the Matilda HPC Cluster
• Logging into Matilda with MobaXterm
• Logging into Matilda with PuTTY
• HPC Modules Software System
• Available HPC Software
• HPC Launching Jobs
• HPC SBATCH Options
• Job Script Examples
• HPC Using Job Steps

MPI Parallel Processing

• MPI on Matilda
• OpenMPI
• MPICH -- can't access article

Data Management

• Matilda HPC Cluster Storage
• Moving Files
• Scratch File Management
• Globus Data Transfers
• TMP Space Management
• Scratch Space Monitoring
• Granting Special Permissions
• Changing Default Permissions

Job and Account Monitoring

• SLURM Monitoring Commands
• HPC Powertools
• On-Node Monitoring

Application Specific Help

• AlphaFold
• Conda Essentials
• Conda: Importing/Exporting Environments
• Converge and Converge Studio
• DMTCP
• Gaussian
• GNU Parallel
• Using Jupyter Notebook and Lab on Matilda
• Using MPI with Jupyter Notebook
• Using Slurm with Jupyter Notebook
• LabGym
• MATLAB
• Singularity and Docker Containers
• ProkSeq
• Visit

Troubleshooting

• Conda and Python

MATLAB Installation Help

• MATLAB Installation

Mathematica Help

• Mathematica Online Comprehensive Site
• Mathematica Site Network
• Mathematica Home License

System Status

• HPC Change Log
• HPC Feature Updates

MSU ICER HPCC Buy-in

• MSU HPCC Buy-in Nodes