Tutorials

Description:

This training provides an overview of the LSU and LONI HPC general account and allocation policies, hardware and software environments, queuing system, compiling programs, writing submit scripts, running and monitoring jobs on HPC systems.

This training is a mandatory two-day training event for all LSU and LONI HPC new users.

Prerequisites:

1) Access to a Linux based computer, i.e., Linux (Any distribution), Mac OSX, or Windows with Windows Subsystem for Linux (WSL) installed.
2) Familiarity with Linux/Unix commands and editors.

Description:

This training provides an overview of the LSU and LONI HPC general account and allocation policies, hardware and software environments, queuing system, compiling programs, writing submit scripts, running and monitoring jobs on HPC systems.

This training is a mandatory two-day training event for all LSU and LONI HPC new users.

Prerequisites:

1) Access to a Linux based computer, i.e., Linux (Any distribution), Mac OSX, or Windows with Windows Subsystem for Linux (WSL) installed.
2) Familiarity with Linux/Unix commands and editors.

Description:

For anyone who works in a Linux/Unix environment, a working knowledge of shell scripting is essential and will boost their efficiency and productivity tremendously. For this tutorial, we will focus on bash as it is one of the most popular shells. This tutorial will include topics such as creating simple bash scripts, flow control, command line arguments, regex, grep, awk and sed. This is a practical tutorial, so we will provide examples and/or hands-on exercises for most of the covered materials.

Prerequisites:

1) Access to a Linux based computer, i.e., Linux (Any distribution), Mac OSX, or Windows with Windows Subsystem for Linux (WSL) installed.
2) Familiarity with Linux/Unix commands and editors.

Description:

This training will provide an introduction to Open OnDemand, a browser-based tool now available to all LSU HPC users on campus. Open OnDemand requires only a web browser (no plug-ins) and an HPC account. It features a file browser, command line shell access, job management, and access to interactive Jupyter notebooks and RStudio servers running interactively on HPC cluster's compute nodes.

Prerequisites:

Basic knowledge of HPC environment and Linux is preferred but not required.

Description:

The purpose of this training is to familiarize LSU researchers with Tiger Den, the on‑campus research data storage solution. Tiger Den provides a total capacity of 3 PB and up to 1 TB of free storage for LSU-affiliated researchers, and offers a secure, centrally managed environment for storing research datasets. The session guides participants through the process of requesting an account, navigating the Tiger Den management portal, and using the system effectively. This training is intended for faculty and research staff seeking reliable, cost‑effective data storage solutions.

Prerequisites:

Description:

Installing and managing software packages often poses a challange to HPC users on Linux systems without root permission. This two-part mini series is aiming at introducing helpful tools to remedy that.

This part will feature container technology and the software Singularity (a.k.a. Apptainer), a popular implementation of containers on HPC. Containers are gaining increasing popularities for its flexibility and portability. More and more developers now start to release their software packages as working containers for users' convenience. In this training, we will discuss how to use Singularity to run container images on our clusters, acquire more container images, and build your own container images. We will also showcase the usage of containerized popular packages such as Tensorflow and PyTorch.

Prerequisites:

Basic knowledge of HPC environment and Linux is preferred but not required.

Description:

Installing and managing software packages often poses a challange to HPC users on Linux systems without root permission. This two-part mini series is aiming at introducing helpful tools to remedy that.

This part will feature virtual environments and the software Conda, a popular tool working with virtual environments. In this training, we will discuss how to use Conda and virtual environments to install and manage software packages on our clusters, including frequently requested packages such as Tensorflow and PyTorch. We will also share useful tips, such as sharing virtual environment with group members and using Conda to manage software packages beyond Python (e.g., R / Perl).

Prerequisites:

Basic knowledge of HPC environment and Linux is preferred but not required.

Description:

In scientific computing disciplines such as bioinformatics, computational biology, and other data-intensive fields, many tools and workflows remain serial in nature. Running a large number of these independent jobs efficiently on a multi-core HPC platform can be challenging.

This training will introduce two powerful approaches for handling such workloads namely GNU Parallel and SLURM Job Arrays. This training session covers efficient execution and management of large collections of independent or parameter-sweep tasks using GNU Parallel and SLURM Job Arrays, leveraging both single-node and multi-node HPC environments for scalable, high-throughput processing. Through hands-on, real-world examples, we will demonstrate how to launch, monitor, and optimize massive batches of serial or lightweight jobs using GNU Parallel and SLURM Job Arrays, highlighting their similarities, differences, and best-use scenarios.

Prerequisites:

Basic knowledge of HPC environment and Linux is preferred but not required.

Description:

Molecular dynamics simulation (MD) is a computational technique that is used to study the dynamics of molecules and atoms over time. The tutorial will discuss the essentials of the classical molecular dynamics simulations. The basic system setup, initialization, and analysis for widely used simulation packages such as LAMMPS, GROMACS, AMBER and NAMD on LONI and LSU HPC clusters will be reviewed.

Prerequisites:

Basic knowledge of HPC environment and Linux is preferred but not required.