Courses
Last Updated: October 4, 2024
Every semester, Texas A&M High Performance Research Computing (HPRC) offers short courses covering a range of topics for beginning, intermediate, and advanced researchers. The semesters start with hour-long "primer" courses. These primers cover material that is prerequisite to ALL other short courses. These, along with courses on the clusters and schedulers form the basis for using the respective clusters effectively. 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 2024
Introduction to PETSc: A Hands-on Workshop
Instructor: Iman Borazjani
Time: Friday, October 11, 2024 — 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.
Prerequisites: Active HPRC account
Introduction to Perl
Instructor: Keith Jackson
Time: Friday, October 11, 2024 — 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.
Prerequisites: Active HPRC account
ACES: Fundamentals of Containers
Instructor: Richard Lawrence
Time: Tuesday, October 15, 2024 — 10:00AM-12:30PM 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.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills
ACES: AI/ML on Intel PVC GPUs
Instructor: Zhenhua He
Time: Tuesday, October 15, 2024 — 1:30PM-4:00PM 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.
Prerequisites: 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
RNA-seq and Differential Expression
Instructor: Wesley Brashear
Time: Friday, October 18, 2024 — 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.
Prerequisites: Active HPRC account
ACES: Containers for Scientific Workflows (Singularity / Apptainer)
Instructor: Richard Lawrence
Time: Tuesday, October 22, 2024 — 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.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills. Python skills recommended.
ACES: Introduction to CryoSPARC for Cryo-EM Data Processing in Collaboration with the Laboratory for Biomolecular Structure and Dynamics
Instructor: Michael Dickens, Gaya Yadav
Time: Tuesday, October 22, 2024 — 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.
Prerequisites: Current ACCESS ID, CryoSPARC Academic License ID
Introduction to Next Generation Sequencing Analysis
Instructor: Michael Dickens
Time: Friday, October 25, 2024 — 10:00AM-12:30PM CT
Location: Blocker 220
Description: Covers concepts of sequence mapping, variant calling and ChIP-seq analysis utilizing tools available on the HPRC clusters.
Prerequisites: Active HPRC account
AlphaFold Protein Structure Prediction
Instructor: Michael Dickens
Time: Friday, October 25, 2024 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: This course provides an introduction to using AlphaFold for protein structure prediction on Grace.
Prerequisites: Active HPRC account, basic Linux/Unix skills
ACES: Containers for Scientific Workflows (Charliecloud)
Instructor: Richard Lawrence
Time: Tuesday, October 29, 2024 — 10:00AM-12:30PM CT
Location: Online using Zoom
Description: This course introduces the use of Containers using the Charliecloud software suite. Exercises will be performed using the ACES cluster, a composable accelerator testbed at Texas A&M University.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills
ACES: Introduction to Julia
Instructor: Wes Brashear
Time: Tuesday, October 29, 2024 — 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.
Prerequisites: Current ACCESS ID
ACES: NGS Metagenomics
Instructor: Wesley Brashear
Time: Tuesday, November 5, 2024 — 10:00AM-12:30PM CT
Location: online using Zoom
Description: This short course introduces concepts of metagenomics analysis based on data generated by Next Generation Sequencing (NGS) technology using the ACES cluster.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills, and basic familiarity with NGS techniques/terminology
ACES: Rust
Instructor: Jian Tao
Time: Tuesday, November 12, 2024 — 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.
Prerequisites: Current ACCESS ID; Basic understanding of programming concepts (variables, loops, functions), Familiarity with any programming language
ACES: GPU Programming
Instructor: Jian Tao
Time: Tuesday, November 12, 2024 — 1:30PM-4:00PM 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.
Prerequisites: Current ACCESS ID, Linux/Unix skills, experience with C or C++
HPRC Primers
Instructor: Minh Nguyen, Aakashdeep Sil, Trenton Gray, Andrii Kryvenko, Surada Suwansathit, Keegan Smith
Time: August 27, August 30, and September 3, 2024
Location: Online using Zoom
Description: These hour long primers are designed to cover basic topics.
Prerequisites: Current ACCESS ID or HPRC account (see 'Topics' section for details)
Introduction to Linux
Instructor: Wes Brashear
Time: Friday, September 6, 2024 — 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.
Prerequisites: Active HPRC account
Introduction to HPRC Computing Resources
Instructor: Josh Winchell
Time: Friday, September 6, 2024 — 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.
Prerequisites: Basic Linux/Unix skills, active HPRC account
ACES: Introduction to Composable Computing on ACES and FASTER
Instructor: Josh Winchell
Time: Tuesday, September 10, 2024 — 10:00AM-12:30PM CT
Location: Online using Zoom
Description: Introduction to research computing on the composable ACES and FASTER clusters. Topics covered include hardware, access, policies, file systems, and batch processing.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills
ACES: Using the Slurm Scheduler on Composable Resources
Instructor: Michael Dickens
Time: Tuesday, September 10, 2024 — 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.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills
Intermediate Linux
Instructor: Wes Brashear
Time: Friday, September 13, 2024 — 10:00AM-12:30PM CT
Location: Blocker 220
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.
Prerequisites: Active HPRC account, basic Linux/Unix skills
Applying for Accounts on HPRC Clusters
Instructor: Sandra Nite and Sheri Stebenne
Time: Friday, September 13, 2024 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: Descriptions of the types of accounts on the HPRC clusters will be explained. Requirements for applications for accounts will be discussed. We will allocate time for a Q&A session at the end.
Prerequisites: None
ACES: AI TechLab in Jupyter Notebooks
Instructor: Zhenhua He
Time: Tuesday, September 17, 2024 — 10:00AM-12:30PM 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.
Prerequisites: Current ACCESS ID, Python
ACES: Introduction to OpenFOAM
Instructor: Björn Windén
Time: Tuesday, September 17, 2024 — 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.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills. C++ experience recommended.
Introductory and Intermediate Python for Data Science
Instructor: Richard Lawrence
Time: Sessions 1 and 2 — Friday, September 20 and 27, 2024 — 9:00AM-4:00PM CT (with a one hour lunch break)
Location: Blocker 220
Description: A two-part introduction to programming with Python. These two Friday sessions will cover programming basics and introduce data structures and operations used in Python. Suggested starting place for people new to programming or Python.
Prerequisites: None
ACES: Introduction to Data Science in R
Instructor: Wesley Brashear
Time: Tuesday, September 24, 2024 — 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.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills
ACES: Graphcore IPU Tutorial
Instructor: Zhenhua He
Time: Tuesday, October 1, 2024 — 10:00AM-12:30PM CT
Location: Online using Zoom
Description: This short course introduces researchers to Graphcore Intelligence Processing Units (IPUs) on the ACES cluster, a composable accelerator testbed. The instructor will demonstrate the execution of models from different frameworks on the IPU system, and participants will gain practical experience in converting TensorFlow and PyTorch code into IPU code through hands-on exercises.
Prerequisites: 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: AlphaFold Protein Structure Prediction
Instructor: Michael Dickens
Time: Tuesday, October 1, 2024 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: This course provides an introduction to using AlphaFold for protein structure prediction on ACES.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills
Fundamentals of R Programming
Instructor: Wesley Brashear
Time: Friday, October 4, 2024 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.
Prerequisites: Active HPRC account, Linux/Unix skills
Introduction to OpenFOAM
Instructor: Björn Windén
Time: Friday, March 22, 2024 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: Introduction to OpenFOAM, the open source CFD Toolbox, and how to use it on HPRC clusters.
Prerequisites: Active HPRC account, basic Linux/Unix skills. C++ experience recommended.
ACES: Introduction to PyFR, a Scalable Open-source CFD Flow Solver
Instructor: Sambit Mishra
Time: Tuesday, March 26, 2024 — 10:00AM-12:30PM CT
Location: online using Zoom
Description: Beginner-level skills for running PyFR simulations on clusters
Prerequisites: Current ACCESS ID, basic Linux/Unix skills, basic Python skills.
Using MATLAB on the ACES Cluster
Instructor: Marinus Pennings
Time: Tuesday, April 16, 2024 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: This course introduces different ways to use MATLAB on the ACES cluster and how to leverage its parallel resources.
Prerequisites: Current ACCESS ID, basic knowledge of MATLAB
ACES: NEC Vector Annealing
Instructor: Raghunandan Mathur
Time: Tuesday, November 28, 2023 — 10:00AM-12:30PM CT
Location: online using Zoom
Description: Introduction to quantum inspired techniques to solve NP Hard problems and combinatorial optimization using HPC hardware. A starter to NEC's Vector Annealing (VA) library on the ACES cluster with hands-on exercises on real world use cases.
Prerequisites: Current ACCESS ID, basic Python skills, basic understanding of Linear Algebra
Using MATLAB on the Grace Cluster
Instructor: Marinus Pennings
Time: Friday, September 29, 2023 — 10:00AM-12:30PM CT
Location: Blocker 220
Description: This course introduces different ways to use MATLAB on the Grace cluster and how to leverage its parallel resources.
Prerequisites: Active HPRC account, basic knowledge of MATLAB
ACES: RNA-seq and Differential Expression
Instructor: Wesley Brashear
Time: Tuesday, October 31, 2023 — 10:00AM-12:30PM CT
Location: online using Zoom
Description: Covers a brief introduction to RNA-seq technology, NGS QC, and differential expression analysis/data visualization.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills, and basic familiarity with NGS techniques/terminology
ACES: NVIDIA Parabricks
Instructor: Greg Zynda
Time: Tuesday, October 31, 2023 — 1:30PM-4:00PM CT
Location: online using Zoom
Description: Introduction to NVIDIA Parabricks, a software suite that allows users to perform secondary analysis of next generation sequencing DNA and RNA data. The software incorporated into NVIDIA Parabricks has been optimized to run on GPUs, drastically increasing the speed at which common NGS analyses and tasks can be completed.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills, and basic familiarity with NGS techniques/terminology
Intermediate R Programming
Instructor: Wesley Brashear
Time: Friday, Apr 28, 2023 10:00AM-4:00PM CT (with a one hour lunch break)
Location: Blocker 220
Description: This course covers intermediate concepts in the R programming language and can be taken as a stand-alone course or after completion of the Fundamentals of R programming course.
Prerequisites: Basic knowledge of R/RStudio
Introduction to CryoSPARC for Cryo-EM Data Processing on HPRC in Collaboration with BCBP Cryo-EM Research Center
Instructor: Michael Dickens, Gaya Yadav
Time: Friday, Apr 14, 2023 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: This course will cover aspects of using CryoSPARC on HPRC resources including accessing CryoSPARC on the Grace cluster followed by a demonstration with example image files.
Prerequisites: Active HPRC account, CryoSPARC Academic License ID
Intermediate Linux for FASTER/ACES
Instructor: Andrew Palughi
Time: Tuesday, September 27, 2022 — 10:00AM-12:30PM CT
Location: online using Zoom
Description: Topics 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.
Prerequisites: Current ACCESS ID, basic Linux/Unix skills
Slurm Job Scheduling
Instructor: Michael Dickens
Time: Friday, September 30, 2022 — 10:00AM-12:30PM CT
Location: Blocker 220 and online using Zoom
Description: Covers various job scheduling approaches using the Slurm Workload Manager on Grace.
Prerequisites: Active HPRC account, Linux/Unix skills
Microcredentials in Research Computing
Instructor: Richard Lawrence
Time: Friday, September 30, 2022 — 1:30PM-4:00PM CT
Location: Blocker 220 and online using Zoom
Description: During this short course, instructors will discuss opportunities to earn micro-credentials developed by Texas A&M High Performance Research Computing.
Prerequisites: None
Introduction to LAMMPS for ACES
Instructor: Andrew Palughi
Time: Tuesday, October 4, 2022 — 1:30PM-4:00PM
Location: online using Zoom
Description: This short course provides an introduction to atomistic modeling of materials with classical potentials using LAMMPS.
Prerequisites: Current ACCESS ID or HPRC account
Technology Lab: FEA with moose
Instructor: Andrew Palughi
Time: Tuesday, October 18, 2022 — 10:00AM-12:30PM CT
Location: online using Zoom
Description: This short course provides an introduction to using MOOSE for finite element analysis. Attendees will learn how to setup and use MOOSE on HPRC clusters. This course will involve hands-on exercises so attendees can gain experience using the software. These exercises will involve using FEA to solve models of thermal transport.
Prerequisites: Current ACCESS ID or HPRC account
ACES: Intel AI/ML Training
Instructor: HPRC: Richard Lawrence, Zhenhua He; Intel: Aaryan Kothapalli, Yuning Qiu
Time: Tuesday, October 25, 2022 and Tuesday, November 1, 2022 — 10:00AM-12:30PM CT and 1:30PM-4:00PM CT
Location: online using Zoom
Description: In this two-day workshop, you will learn about several components available inside the oneAPI Toolkit for AI/ML applications.
Prerequisites: Current ACCESS ID or HPRC account, experience with python
ACES: Using FPGAs
Instructor: Abhinand Nasari and Shaina Le
Time: Tuesday, November 29, 2022 — 1:30PM-4:00PM CT
Location: Zoom session
Description: This course will introduce students to the Intel FPGAs and how to use the Intel oneAPI toolkit to develop applications to run on FPGAs.
Prerequisites: Current ACCESS ID or HPRC accountk, basic Linux/Unix skills, C++
NGS Metagenomics
Instructor: Wesley Brashear
Time: Friday, December 2, 2022 10:0AM-12:30PM CT
Location: Blocker 220
Description: This short course introduces concepts of metagenomics analysis based on data generated by Next Generation Sequencing (NGS) technology.
Prerequisites: Active HPRC account
Drug Docking with Schrodinger
Instructor: Xin Yang
Time: Friday, February 11, 2022 — 1:30PM-4:00PM CT
Location: Blocker 220 and online using Zoom
Description: This course introduces the basic concepts behind computer aided drug design (CADD) with an emphasis on structure-based virtual screening using Schrödinger's Glide and CovDock packages.
Prerequisites: Active HPRC account, basic Linux, and Molecular Biochemistry knowledge
Introduction to Scientific Python
Instructor: Zhenhua He
Time: Friday, February 18, 2022 — 1:30PM-4:00PM CT
Location: Blocker 220 and online using Zoom
Description: This short course covers several topics and packages for scientific programming in Python.
Prerequisites: Active HPRC account, basic Python skills
Introduction to Quantum Chemistry Simulations with ORCA
Instructor: Xin Yang
Time: Friday, February 25, 2022 — 10:00AM-12:30PM CT
Location: Blocker 220 and online using Zoom
Description: Covers basic concepts in quantum chemistry simulations and offers hands-on opportunities to perform standard calculations using ORCA.
Prerequisites: Active HPRC account, Basic Linux and Physical Chemistry knowledge
ORCA - Transition State and Advanced Topics
Instructor: Xin Yang
Time: Friday, February 25, 2022 — 1:30PM-4:00PM CT
Location: Blocker 220 and online using Zoom
Description: Covers reaction mechanism studies using quantum chemistry simulations.
Prerequisites: Active HPRC account, Introduction to Quantum Chemistry Simulations with ORCA
Python Tools for Geosciences
Instructor: Abishek Gopal
Time: Friday, April 1, 2022 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: This short course will introduce some basic Python packages relevant to Geoscientific data analysis.
Prerequisites: Active HPRC account, experience with Python or scientific programing languages (MATLAB, NCL etc), some experience with data structures and Jupyter notebooks is recommended
Introduction to Fortran
Instructor: Abishek Gopal
Time: Friday, April 8, 2022 — 10:00AM-12:30PM CT
Location: Blocker 220
Description: Covers basic topics in numerical computation and scientific programming using Fortran 90/95. Topics include basic language elements and concepts, intrinsic functions and usage, programming best practice, and relevant open source tools. This is a basic to intermediate level course.
Prerequisites: Active HPRC account
Introduction to Code Parallelization using OpenMP
Instructor: Marinus Pennings
Time: Opens Friday, April 8, 2022
Location: Google Classroom
Description: Covers code parallelization for shared memory systems using the OpenMP standard of directives and calls.
Prerequisites: Current Ada account, working knowledge of C/C++ or FORTRAN, Intro to Linux or Linux/Unix skills
Introduction to Code Parallelization using MPI
Instructor: Marinus Pennings
Time: Opens Friday, April 8, 2022
Location: Google Classroom
Description: Covers basic concepts in MPI, including distributed memory systems, messages, blocking/non-blocking, point-to-point communication, collective communication.
Prerequisites: Active HPRC account, working knowledge of C/C++ or FORTRAN