Tutorials

HPC@LSU invites you to attend our weekly training scheduled every Wednesdays, except university holidays.

Due to concern about the COVID-19 pandemic, all training sessions are pure Zoom online events from 9:00AM to 11:00AM. The sessions will be available only for remote participants and will be recorded for later review.

The training sessions are subject to cancellation due to lack of registrations, so please register if you plan on attending. Registration closes in the afternoon on the day prior to the training.

Click on the tutorial topic to obtain more information and registration details. Remote connect links to attend the training will be provided via email to all registered participants.

Note: The Slide and Support Materials links are placeholders until content is added after the tutorial.

Spring 2024 Training Schedule

1. February 28,2024: Introdution to Python

TopicIntrodution to Python
DateFebruary 28,2024
Time9:00 AM - 11:00 AM
PlaceZoom Online
DescriptionPython is a high-level programming language, easy to learn yet extremely powerful. This training will provide an introduction to programming in Python. The subjects include basic Python syntax, Python classes used in object-oriented programming. Basic Python modules for scientific computing and plotting will also be introduced. During the training, simple Python programs will be provided for demonstration.

Prerequisites
  • Basic understanding of a programming language is assumed but not required.

Slides
RegistrationClick here

2. March 06,2024: Magic Tools to Install & Manage Software Part 1: Conda Virtual Environment

TopicMagic Tools to Install & Manage Software Part 1: Conda Virtual Environment
DateMarch 06,2024
Time9:00 AM - 11:00 AM
PlaceZoom Online
DescriptionInstalling 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.

Part 1 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).

* Materials has been updated to reflect a recent major Conda update in Jul 2023. Users are recommended to take / review the training even if they used conda before.


Prerequisites
  • Basic understanding of shell commands is assumed but not required.

RegistrationClick here

3. March 20,2024: Magic Tools to Install & Manage Software Part 2: Singularity Container

TopicMagic Tools to Install & Manage Software Part 2: Singularity Container
DateMarch 20,2024
Time9:00 AM - 11:00 AM
PlaceZoom Online
DescriptionInstalling 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.

Part 2 will feature container techenology 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 understanding of the Linux OS and shell commands is assumed but not required.

Slides
RegistrationClick here

4. March 27,2024: Introduction to GNU Parallel

TopicIntroduction to GNU Parallel
DateMarch 27,2024
Time9:00 AM - 11:00 AM
PlaceZoom Online
DescriptionIn scientific computation disciplines, such as bioinformatics and computational biology, many computational tools are serial in nature. To effectively run many serial jobs simultaneously on multi-core HPC platform can be challenging. GNU Parallel is an easy to use and also powerful tool for executing commands/tasks in parallel on one or multiple host machines. This training will introduce GNU Parallel and its basic features. Hand-on, real-world examples will be demonstrated on how to run different types of massive individual tasks using GNU Parallel.
Prerequisites
  • Basic knowledge of HPC environment and Linux is preferred but not required.

Slides
Source Code
RegistrationClick here

5. April 03,2024: Open OnDemand: Interactive HPC via the Web

TopicOpen OnDemand: Interactive HPC via the Web
DateApril 03,2024
Time9:00 AM - 11:00 AM
PlaceZoom Online
DescriptionThis 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 LSU 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 SuperMIC's compute nodes. This training will feature an overview of Open OnDemand, and a demonstration of all it's features, including Jupyter Notebook and RStudio.

Prerequisites
  • LSU HPC account
  • Some knowledge of using HPC is assumed but not required

Slides
RegistrationClick here

6. April 10,2024: Molecular Dynamics

TopicMolecular Dynamics
DateApril 10,2024
Time9:00 AM - 11:00 AM
PlaceZoom Online
DescriptionMolecular 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.

RegistrationClick here

HPC Training Survey

We value your feedback, and will use your feedback to help improve our HPC training offerings. Please complete a short survey at the end of each training using this link.

Past Tutorials

We offer many tutorial sessions for our users both on campus and online. The training topics include but are not limited to:

  • Introduction to Linux
  • HPC user environment
  • Version control with git
  • Pythong and R programming
  • Deep learning basics
  • Parallel programming

To read descriptions or access PDF's of the slides from past tutorials Past Tutorials.