 Research Computing

This is a comprehensive list of software modules available on Matilda, including licensed tools.

An explanation of Matilda HPC Cluster accounts & a guide to requesting one.

Log of software installations, updates installed, planned maintenance, configuration changes.

This article explains how to use Conda on the Matilda HPC cluster to create, manage, and troubleshoot custom software environments.

This article explains how to run Converge and Converge Studio on the Matilda HPC cluster, including GUI setup, SLURM job submission, and resource configuration for simulations.

Significant features additions and changes related to the Matilda HPC cluster are provided herein by the date they were introduced.

This article explains how to run Gaussian on Matilda HPC using CPU or GPU builds, including how to match job script and input file settings for successful execution.

This article explains how to use Globus to securely transfer and share large datasets with Matilda HPC and external systems.

This article explains how to use Access Control Lists (ACLs) on Matilda to manage fine-grained file and directory permissions for users and groups in scratch spaces.

This article explains how to write and submit different types of Slurm job scripts on the Matilda HPC Cluster.

This article explains how to set up and run LabGym on Matilda using a personal installation directory for user-specific detectors and models.

This article introduces the use of the Slurm Workload Manager on the Matilda HPC Cluster.

This document presents a procedure for logging into the Matilda Cluster with SSH using the PuTTY Windows client.

This article explains how eligible Oakland University faculty and staff can request access to the Matilda HPC Cluster.

This article explains how to access and activate Wolfram Mathematica through various license options, including on-campus, home, and cloud-based versions.

This article explains how to configure and run MATLAB jobs on the Matilda HPC cluster.

This article explains how to download, install, and activate MATLAB using the university’s campus-wide license, including guidance for both individual and shared (concurrent) installations.

This article explains how to use the Environment Modules system on Matilda to load, manage, and reset software environments for HPC workflows.

This article is about how to correctly run OpenMPI applications on Matilda HPC, covering best practices, common pitfalls, and options for interactive or batch job execution using mpirun.

This article is about Powertools, a set of simple commands on Matilda that help users monitor jobs, storage, and account usage without needing to learn SLURM.

This article explains how to load and configure ProkSeq on Matilda, set up input files, and run example jobs interactively or in batch mode.

Information regarding various options for SBATCH and SRUN.

This article explains how to check for old files in scratch space that might get deleted soon and how to set up daily reminders to stay ahead of it.

This article explains how to set up a daily cron job on Matilda to monitor scratch space for files older than a set number of days and get notified before they're auto-deleted.

This article shows how to run Docker containers with Singularity on Matilda, either interactively or through batch jobs.

An explanation of Matilda HPC Cluster storage and how much is provided.

This article explains how to manage and reassign temporary file storage on Matilda to avoid space errors, with important cautions for MPI job compatibility.

This article explains how to view, temporarily change, or permanently modify the default file and directory permissions on Matilda using the umask setting.

This article explains how to run AlphaFold on the Matilda HPC cluster, including module setup, database access, and GPU usage for optimal performance.

This article explains how to use Job Steps in SLURM to run parallel or sequential tasks within a single job script using srun.

This article explains how to set up and run Jupyter Notebook or Jupyter Lab on Matilda HPC using conda environments.

This article explains how to run MPI-based Jupyter Notebooks on Matilda HPC using conda, ipyparallel, and mpi4py with a multi-node SLURM job.

This article demonstrates how to launch SLURM jobs from a Jupyter Notebook session.

This article explains how to install and configure the VisIt application

An explanation of what Matilda HPC Cluster is.

Procedure on upgrading Adonis.