Courses
Last Updated: October 21, 2025
Every semester, Texas A&M High Performance Research Computing (HPRC) offers short courses covering a range of topics for beginning, intermediate, and advanced researchers. Courses taught early in the semester on the clusters and schedulers form the basis for using the respective clusters effectively. We also offer short "primer" classes taught throughout the semester to brush up on basics quickly. All courses will be delivered in an interactive style through a live login session. In general, slides and other supplemental materials are available on each course page.
Registration is required for each primer or short course. Attendees will need to use their own device. Workstations are not provided. The typical short course runs for 2.5 hours, unless otherwise noted. Each primer runs for 1 hour.
Most courses will require one of two accounts:
- Courses on the Grace cluster require an HPRC account. To apply for an account, please review the policies at hprc.tamu.edu/policies and apply at hprc.tamu.edu/apply.
- Courses on the ACES cluster require an ACCESS ID, which individuals from both TAMU and other institutions can get at operations.access-ci.org/identity/new-user (scroll down the page). A walkthrough of the application process can be found at https://hprc.tamu.edu/kb/Helpful-Pages/ACCESS-ID/. To learn more about ACCESS, please visit access-ci.org.
In-class short courses have a seating limit of about 45 students.
For our course offerings from previous semesters, please consult this page.
Short Course List for Fall 2025
Data Science meets Geoscience: a Case Study in Rock Weathering and Riverine Carbon Fluxes
Instructor(s): Shihan Li, Xiying Sun, and Yating Li
Time: Friday, October 24, 2025 — 10:00AM-12:30PM CT
Location: Blocker 220 and online via Zoom
Description: This short course aims to provide an intuitive understanding of data science and its applications in geoscience and carbon cycle research
Prerequisite(s): Active ACCESS ID; familiarity with Jupyter Notebook; basic programming skills recommended
View Details In-Person Attendee Registration Remote Attendee Registration
Incorporating Snakemake in HPC Workflows
Instructor(s): Dr. Wes Brashear
Time: Friday, October 24, 2025 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: Snakemake is a Python-based workflow management system for creating reproducible and scalable data science pipelines. Students will learn best practices on how to incorporate Snakemake in their workflows on HPRC systems and complete hands-on exercises creating simple Snakemake workflows to more complex, multi-step pipelines culminating in descriptive workflow reports.
Prerequisite(s): Active HPRC account
ACES: Introduction to Data Science in R
Instructor(s): Dr. Wesley Brashear
Time: Tuesday, October 28, 2025 — 10:00AM-4:00PM CT (with a one hour lunch break)
Location: Online using Zoom
Description: This course is an introduction to the R programming language and covers the fundamental concepts needed to operate in the R environment. Students are not required to have any prior experience with R.
Prerequisite(s): Current ACCESS ID, basic Linux/Unix skills
ACES: Containers for Scientific Workflows (Singularity / Apptainer)
Instructor(s): Richard Lawrence
Time: Friday, October 31, 2025 — 10:00AM-12:30PM CT
Location: Online using Zoom
Description: This course introduces the use of containers for scientific workflows using the Singularity container engine. Exercises will be performed using the ACES cluster, a composable accelerator testbed at Texas A&M University.
Prerequisite(s): Current ACCESS ID, basic Linux/Unix skills. Python skills recommended.
ACES: Introduction to OpenFOAM
Instructor(s): Dr. Björn Windén
Time: Friday, October 31, 2025 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: Introduction to OpenFOAM, the open source CFD Toolbox, and how to use it on HPRC clusters.
Prerequisite(s): Current ACCESS ID, basic Linux/Unix skills.
ACES: GPU Programming
Instructor(s): Jian Tao
Time: Tuesday, November 4, 2025 — 10:00AM-12:30AM CT
Location: Online using Zoom
Description: Covers basic topics in CUDA programming on NVIDIA GPUs. Topics include CUDA architecture; basic language usage of CUDA C/C++; writing, executing CUDA code.
Prerequisite(s): Current ACCESS ID, Linux/Unix skills, experience with C or C++
ACES: Introduction to CryoSPARC for Cryo-EM Data Processing in Collaboration with the Laboratory for Biomolecular Structure and Dynamics
Instructor(s): Dr. Michael Dickens, Dr. Gaya Yadav
Time: Tuesday, November 4, 2025 — 1:30PM-4:00PM CT
Location: online using Zoom
Description: This course will cover aspects of using CryoSPARC on the ACES cluster followed by a training session using example image files.
Prerequisite(s): Current ACCESS ID, CryoSPARC Academic License ID
Primer: Running Jupyter Notebook on the ACES Portal
Instructor(s): Siddhi Mittal
Time: Friday, November 7, 2025 10:00AM-11:00AM CT
Location: Online using Zoom
Description: A live session on starting and using a Jupyter notebook in Open OnDemand on HPRC clusters. Class conducted on ACES.
Prerequisite(s): Active ACCESS ID
Primer: AI Coding Assistant
Instructor(s): Keegan Smith
Time: Friday, November 7, 2025 1:30PM-2:30PM CT
Location: Online using Zoom
Description: This course is a hands-on introduction to using the Jupyter AI Assistant on Texas A&M's ACES cluster. Attendees will launch a session via Open OnDemand, load the provided notebook, choose the HPRC-hosted model, and complete four short labs.
Prerequisite(s): Active ACCESS ID
ACES: AI/ML TechLab on Graphcore IPUs
Instructor(s): Dr. Zhenhua He
Time: Tuesday, November 11, 2025 — 10:00AM-12:30PM CT
Location: Online using Zoom
Description: This course introduces researchers to Graphcore Intelligence Processing Units (IPUs) on the ACES cluster, a composable accelerator testbed. The instructor will lead participants through the execution of models from different frameworks on the IPU system. Participants will gain practical experience in converting TensorFlow and PyTorch code into IPU code through hands-on exercises.
Prerequisite(s): Current ACCESS ID; basic Linux/Unix skills; basic understanding of machine learning concepts, neural networks, and deep learning; familiarity with deep learning frameworks TensorFlow and/or PyTorch
ACES: Introduction to CuPy: NumPy & SciPy for GPU
Instructor(s): Jian Tao
Time: Tuesday, November 11, 2025 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: This course covers basic topics in numerical computation and scientific programming using CuPy for GPU acceleration in Python. Topics include CuPy's API (compatible to NumPy and SciPy), device memory and transfers, performance best practices, and relevant open-source tools and workflows.
Prerequisite(s): Current ACCESS ID, basic Python skills
Setting Up Molecular Dynamics Simulations
Instructor(s): Dr. James Mao
Time: Friday, November 14, 2025 10:00AM-12:30PM CT
Location: Blocker 220
Description: This short course provides a step-by-step guide to setting up molecular dynamics (MD) simulations. The course will also cover performing production MD simulations using various software available on the HPRC cluster.
Prerequisite(s): Active HPRC account, active CHARMM-GUI account, basic Linux/Unix skills
Running Molecular Dynamics Simulations Using LAMMPS
Instructor(s): Dr. Dinesh Devarajan
Time: Friday, November 14, 2025 1:30PM-4:00PM CT
Location: Blocker 220
Description: This short course offers a comprehensive, step-by-step guide for setting up and running molecular dynamics (MD) simulations of a variety of systems.
Prerequisite(s): Active HPRC account, basic Linux/Unix skills
Setting up Coding Environments for HPC
Instructor(s): Dr. Thang Ha
Time: Friday, November 21, 2025 10:00AM-12:30PM CT
Location: Blocker 220
Description: In this short course, attendees will learn to set up environments for common AI research workflows involving Python (with PyTorch) and R, as well as set up environments for building and developing software written in compiled languages like C/C++/Fortran.
Prerequisite(s): Active HPRC account,
Introduction to Galaxy for NGS analysis
Instructor(s): Dr. Michael Dickens
Time: Friday, November 21, 2025 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: Covers usage and best practices for HPRC Maroon Galaxy.
Prerequisite(s): Active HPRC account
ACES: Python for Data Scientists
Instructor(s): Richard Lawrence
Time: Tuesday, November 25, 2025 — 10:00AM-4:00PM CT
Location: Online using Zoom
Description: This short course for experienced programmers introduces the Numpy, Pandas, and Matplotlib libraries commonly used to manage and display large datasets in Python.
Prerequisite(s): Active ACCESS ID, some Python or programming experience
ACES: Introduction to Composable Computing on ACES
Instructor(s): Dr. Josh Winchell
Time: Tuesday, September 2, 2025 — 10:00AM-12:30PM CT
Location: Online using Zoom
Description: Introduction to research computing on the composable ACES cluster. Topics covered include hardware, access, policies, file systems, and batch processing.
Prerequisite(s): Current ACCESS ID, basic Linux/Unix skills
ACES: Using the Slurm Scheduler on Composable Resources
Instructor(s): Dr. Michael Dickens
Time: Tuesday, September 2, 2025 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: Introduction to using the Slurm scheduler on the ACES cluster, a composable accelerator testbed at Texas A&M University. Topics covered include multiple job scheduling approaches and job management tools.
Prerequisite(s): Current ACCESS ID, basic Linux/Unix skills
Primer: Introduction to Linux
Instructor(s): Sahil Vartak
Time: Friday, September 5, 2025 10:00AM-11:00AM CT
Location: Online using Zoom
Description: This primer introduces the basics of working in a Linux environment. The material covered here is a prerequisite to most other courses.
Prerequisite(s): Active HPRC Account
Primer: Introduction to Grace - An HPRC Resource
Instructor(s): Ananya Adiki
Time: Friday, September 5, 2025 1:30PM-2:30PM CT
Location: Online using Zoom
Description: An introduction to HPRC's flagship computing cluster, Grace, shown via a live login session.
Prerequisite(s): Active HPRC account, basic Linux skills
ACES: Software for AI on HPC
Instructor(s): Dr. Zhenhua He and Richard Lawrence
Time: Tuesday, September 9, 2025 10:00AM-12:30PM CT
Location: Online using Zoom
Description: This short course will provide an overview of the resources available on the ACES cluster to support AI workflows and applications. We will introduce a wide range of tools useful for management of software, data, and jobs. Later classes taught by HPRC will expand on individual topics.
Prerequisite(s): Active ACCESS ID, basic Linux/Unix skills
ACES: Applying for Allocations - ACCESS, NAIRR, TAMUS and TAMU
Instructor(s): Dr. Sandra Nite and Sheri Stebenne
Time: Tuesday, September 9, 2025 1:30PM-4:00PM CT
Location: Online using Zoom
Description: This course covers the process of applying for allocations on the ACES testbed high performance cluster at Texas A&M University. This will cover both ACCESS and NAIRR allocations.
Prerequisite(s): None
Introduction to Linux
Instructor(s): Dr. Wes Brashear
Time: Friday, September 12, 2025 — 10:00AM-12:30PM CT
Location: Blocker 220
Description: Topics in this short course include basic commands, process and filesystem concepts, shells, I/O redirection, and shell scripts. The material covered here is a prerequisite to most other courses.
Prerequisite(s): Active HPRC account
Introduction to HPRC Computing Resources
Instructor(s): Dr. Josh Winchell
Time: Friday, September 12, 2025 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: Introduction to using HPRC clusters includes policies, hardware overviews, getting connected, file systems, computing environments, development environments, batch processing, and common problems.
Prerequisite(s): Basic Linux/Unix skills, active HPRC account
ACES: Python for New Programmers
Instructor(s): Dr. Josh Winchell
Time: Tuesday, September 16, 2025 — 10:00AM-4:00PM CT
Location: Online using Zoom
Description: This short course for new programmers (no programming experience required) introduces concepts of programming and the Python programming language. This course will establish a foundation for HPRC courses taught later in the semester that will cover data science and AI in Python.
Prerequisite(s): Current ACCESS ID
Intermediate Linux
Instructor(s): Dr. Wes Brashear
Time: Friday, September 19, 2025 — 10:00AM-12:30PM CT
Location: Blocker 202
Description: This course assumes a working knowledge of the Linux environment. Participants will practice running commands on the Grace cluster, including: vim, sed, awk, grep, bash scripting, and bc. We will also be covering how to customize your environment.
Prerequisite(s): Active HPRC account, basic Linux/Unix skills
Introduction to Next Generation Sequencing Analysis
Instructor(s): Dr. Michael Dickens
Time: Friday, September 19, 2025 — 1:30PM-4:00PM CT
Location: Blocker 202
Description: Covers concepts of sequence mapping, variant calling and ChIP-seq analysis utilizing tools available on the HPRC clusters.
Prerequisite(s): Active HPRC account, basic Linux/Unix skills
Primer: Introduction to ACES: A Composable Cluster
Instructor(s): Victor Valdez
Time: Tuesday, September 23, 2025 10:00AM-11:00AM CT
Location: Online using Zoom
Description: An introduction to the composable cluster ACES, covering a variety of topics relevant to computing that are demonstrated through a live login session.
Prerequisite(s): Active ACCESS ID, basic Linux skills
ACES: AI TechLab in Jupyter Notebooks
Instructor(s): Dr. Zhenhua He
Time: Tuesday, September 23, 2025 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: This technology lab contains a set of sessions to help a new user start an AI project on the ACES cluster, a composable accelerator testbed at Texas A&M University.
Prerequisite(s): Current ACCESS ID, basic Python skills
Introduction to PETSc: A Hands-on Workshop
Instructor(s): Iman Borazjani
Time: Friday, September 26, 2025 — 10:00AM-12:30PM CT
Location: Blocker 220
Description: Learn to use PETSc, which can solve large linear or nonlinear systems using advanced iterative techniques on parallel computing clusters.
Prerequisite(s): Active HPRC account; proficiency in a programming language such as C, Fortran, or Python.
NGS Metagenomics
Instructor(s): Dr. Wesley Brashear
Time: Friday, September 26, 2025 1:30PM-4:00PM CT
Location: Blocker 220
Description: This short course introduces concepts of metagenomics analysis based on data generated by Next Generation Sequencing (NGS) technology.
Prerequisite(s): Active HPRC account
ACES: Python for Programmers new to Python
Instructor(s): Dr. Josh Winchell
Time: Tuesday, September 30, 2025 — 10:00AM-4:00PM CT
Location: Online using Zoom
Description: This short course for experienced programmers introduces the basic algorithm-oriented and object-oriented programming styles of the Python programming language.
Prerequisite(s): Active ACCESS ID, some prior programming experience
Primer: Introduction to the Drona Workflow Engine
Instructor(s): Kristine Lam
Time: Friday, October 3, 2025 10:00AM-11:00AM CT
Location: Online using Zoom
Description: An introduction to the Drona Workflow Engine: a web-based workflow-creation and job-management tool developed by Texas A&M High Performance Research Computing.
Prerequisite(s): Active ACCESS ID
Primer: Using the Slurm Scheduler
Instructor(s): Owen Schillaci
Time: Friday, October 3, 2025 1:30PM-2:30PM CT
Location: Online using Zoom
Description: This primer covers various job scheduling approaches using the Slurm Workload Manager on the ACES cluster.
Prerequisite(s): Active ACCESS ID, basic Linux skills
ACES: AlphaFold Protein Structure Prediction
Instructor(s): Dr. Michael Dickens
Time: Tuesday, October 7, 2025 — 10:00AM-12:30PM CT
Location: Online using Zoom
Description: This course provides an introduction to using AlphaFold for protein structure prediction on ACES.
Prerequisite(s): Current ACCESS ID, basic Linux/Unix skills
ACES: Introduction to HPC and AI for Faculty and Researchers
Instructor(s): Dr. Zhenhua He and Dr. Dinesh S. Devarajan
Time: Tuesday, Oct 7, 2025 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: This short course will cover the basic concepts and fundamentals of High Performance Computing (HPC), Artificial Intelligence (AI) and why HPC is important for AI. Participants will learn to use scikit-learn and PyTorch libraries to build, train, and evaluate machine learning and deep learning models in JupyterLab on a HPC cluster - ACES.
Prerequisite(s): Active ACCESS ID, basic Python Programming skills, familiarity with PyTorch is preferred but not required
RNA-seq and Differential Expression
Instructor(s): Dr. Wesley Brashear
Time: Friday, Oct 10, 2025 — 10:00AM-12:30PM CT
Location: Blocker 220
Description: Covers a brief introduction to RNA-seq technology, NGS QC, and differential expression analysis/data visualization.
Prerequisite(s): Active HPRC account, basic Linux/Unix skills, and basic familiarity with NGS techniques/terminology
Introduction to Perl
Instructor(s): Keith Jackson
Time: Friday, October 10, 2025 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: Covers basic to intermediate level topics with live illustrations and hands-on exercises using the Jupyter notebook web application.
Prerequisite(s): Active HPRC account
Fundamentals of R Programming
Instructor(s): Dr. Wesley Brashear
Time: Friday, October 17, 2025 10:00AM-4:00PM CT (with a one hour lunch break)
Location: Blocker 220
Description: This course is an introduction to the R programming language and covers the fundamental concepts needed to operate in the R environment. Students are not required to have any prior experience with R.
Prerequisite(s): Active HPRC account
ACES: AI/ML TechLab on Intel PVC GPUs
Instructor(s): Dr. Zhenhua He
Time: Tuesday, October 21, 2025 — 10:00AM-12:30PM CT
Location: online using Zoom
Description: This course provides an overview of Intel PVC GPUs, guidance on accessing these GPUs on the ACES cluster at Texas A&M High Performance Research Computing, and demonstrations of running AI/ML models with the GPUs using PyTorch and Tensorflow.
Prerequisite(s): Current ACCESS ID; basic Linux/Unix skills; basic understanding of machine learning concepts, neural networks, and deep learning; familiarity with deep learning frameworks TensorFlow and/or PyTorch
ACES: Fundamentals of Containers
Instructor(s): Richard Lawrence
Time: Tuesday, October 21, 2025 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: This course introduces concepts of containers and covers common containerization tasks using the Charliecloud and Singularity container engines on the ACES cluster, a composable accelerator testbed at Texas A&M University.
Prerequisite(s): Current ACCESS ID, basic Linux/Unix skills
Quantum Mechanics Simulations of Spectra: IR, Raman, UV-Vis, Fluorescence, NMR
Instructor(s): Dr. James Mao
Time: Friday, February 28, 2025 10:00AM-12:30PM CT
Location: Blocker 220
Description: This short course will provide an introduction to simulating spectra using quantum mechanics calculations. By the end of the course, attendees will be equipped with the skills to simulate and interpret IR, Raman, UV-Vis, and NMR spectra.
Prerequisite(s): Active HPRC account, Linux/Unix skills
ACES: Intro to the Grace Hopper Superchip
Instructor(s): Dr. Dinesh Devarajan
Time: Friday, December 5, 2025 — 10:00AM-12:30PM CT
Location: online using Zoom
Description: In this short-course, we'll explore the technical aspects of the Grace Hopper Superchip, its advantages, challenges, and architectural design. The benchmarks conducted by HPRC researchers will be presented, highlighting the Grace Hopper system's performance across a variety of HPC workloads.
Prerequisite(s): Active ACCESS ID, general understanding of computer architecture
ACES: Introduction to Julia
Instructor(s): Dr. Wes Brashear
Time: Friday, Demcember 5, 2025 — 1:30PM-4:00PM CT
Location: online using Zoom
Description: Covers basic topics in numerical computation and scientific programming using the Julia programming language. Topics include basic language elements and concepts, programming best practice, and relevant open source tools. This is a basic to intermediate level course.
Prerequisite(s): Current ACCESS ID
AlphaFold Protein Structure Prediction
Instructor(s): Dr. Michael Dickens
Time: Friday, March 28, 2025 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: This course provides an introduction to using AlphaFold for protein structure prediction on Grace.
Prerequisite(s): Active HPRC account, basic Linux/Unix skills
Primer: Data Management Practices on HPRC Resources
Instructor(s): Ashwin Kundeti
Time: Friday, April 4, 2025 10:00AM-11:00AM CT
Location: Online using Zoom
Description: This primer covers a variety of topics relevant to data management on HPRC clusters, including transferring data to and from the clusters, data lifecycles, and data policies.
Prerequisite(s): Active HPRC Account, basic Linux/Unix skills
ACES: NGS Metagenomics
Instructor(s): Dr. Wesley Brashear
Time: Tuesday, April 15, 2025 — 1:30PM-4:00PM CT
Location: online using Zoom
Description: This short course introduces concepts of metagenomics analyses based on data generated by Next Generation Sequencing (NGS) technology using the ACES cluster.
Prerequisite(s): Current ACCESS ID, basic Linux/Unix skills, and basic familiarity with NGS techniques/terminology
ACES: Rust
Instructor(s): Jian Tao
Time: Tuesday, April 22, 2025 — 10:00AM-12:30PM CT
Location: online using Zoom
Description: Learn the basics of Rust, a modern systems programming language known for its safety, speed, and concurrency, through hands-on coding exercises and practical examples.
Prerequisite(s): Current ACCESS ID; Basic understanding of programming concepts (variables, loops, functions), Familiarity with any programming language
ACES: Python for HPC and Advanced Topics
Instructor(s): Richard Lawrence
Time: Tuesday, December 2, 2025 — 10:00AM-4:00PM CT
Location: Online using Zoom
Description: This short course for experienced Python programmers will cover several topics relevant to Python workloads running on HPC systems, including environment setup, parallelism, and checkpointing.
Prerequisite(s): Active ACCESS ID, some Python or programming experience