Courses
Last Updated: November 20, 2023
Every semester, HPRC offers short courses ranging in 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. This, 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. Attendants should bring their own laptops as workstations will not be available in the Blocker classroom. In general, slides and other supplemental materials are available on each course page.
Attendees need a valid HPRC account or ACCESS ID, as indicated for each short course, so that they can complete the exercises throughout the training. If you do not have an HPRC account, you can apply at https://hprc.tamu.edu/apply/. If you do not have an ACCESS ID, you can apply at https://identity.access-ci.org/new-user
Registration is required with a classroom seating limit of ~45.
Please bring your own device to follow along during In-Person classes.
The typical Short Course runs for 2.5 hours, unless otherwise noted.
Each Primer runs for 1 hour.
For our course offerings from previous semesters, please consult this page.
Short Course List for Fall 2023
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
HPRC Primers
Instructor: Tanishq Dayma, Akhil Chilumuru, Keegan Smith, Kenton Romero, Ashwin Kundeti, Druva Kumar Gunda, and Amine Sakrout
Time: September 5, 8, and 12, 2023
Location: Online using Zoom
Description: These hour long primers are designed to cover basic topics.
Prerequisites: Current ACCESS ID or HPRC account
Introduction to Linux
Instructor: Wes Brashear
Time: Friday, September 15, 2023 — 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: Current HPRC account
Introduction to HPRC Computing Resources
Instructor: Josh Winchell
Time: Friday, September 15, 2023 — 1:30PM-4:00PM CT
Location: 220 Blocker
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 Unix/Linux skills; current HPRC account.
Introduction to Composable Resources on ACES and FASTER
Instructor: Josh Winchell
Time: Tuesday, September 19, 2023 — 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 19, 2023 — 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
ACES: Introduction to Containers (Charliecloud) Tutorial
Instructor: Richard Lawrence, Zhenhua He, and Wes Brashear
Time: Friday, September 22, 2023 — 10:00AM-12:30PM CT
Location: Blocker 220 or 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
Applying for Accounts on HPRC Clusters - Q&A for Researchers
Instructor: Sandra Nite and Sheri Stebenne
Time: Friday, September 22, 2023 — 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: Fundamentals of R Programming
Instructor: Wesley Brashear
Time: Tuesday, September 26, 2023 — 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. This course assumes no prior experience with R.
Prerequisites: Current ACCESS ID. Basic Unix/Linux skills.
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: Current HPRC account, Basic knowledge of MATLAB
Intermediate Linux
Instructor: Wes Brashear
Time: Friday, September 29, 2023 — 1:30PM-4:00PM 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: Current HPRC account, Basic Linux/Unix
ACES: AI/ML TechLab - Accelerating AI/ML Workflows on a Composable Cyberinfrastructure
Instructor: Zhenhua He
Time: Tuesday, October 3, 2023 — 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: Graphcore IPU Tutorial
Instructor: Alex Tsyplikhin of Graphcore
Time: Tuesday, October 3, 2023 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: This short course introduces researchers to Graphcore IPUs on the ACES cluster, a composable accelerator testbed at Texas A&M University. 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.
Introduction to Next Generation Sequencing Analysis
Instructor: Michael Dickens
Time: Friday, October 6, 2023 — 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: Current HPRC account
AlphaFold Protein Structure Prediction
Instructor: Michael Dickens
Time: Friday, October 6, 2023 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: This course provides an introduction to using AlphaFold for protein structure prediction on Grace.
Prerequisites: Current HPRC account, Basic Linux/Unix skills
ACES: Fundamentals of Containers
Instructor: Richard Lawrence
Time: Tuesday, October 10, 2023 — 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
GPU Programming
Instructor: Jian Tao
Time: Friday, October 13, 2023 — 10:00AM-12:30PM CT
Location: Blocker 220
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 or HPRC account, Unix/Linux skills, experience with C or C++
Introduction to Perl
Instructor: Keith Jackson
Time: Friday, October 13, 2023 — 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: Current HPRC account
ACES: Containers for Scientific Workflows (Singularity / Apptainer)
Instructor: Richard Lawrence
Time: Tuesday, October 17, 2023 — 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. Recommended: Python skills.
Introductory and Intermediate Python for Data Science
Instructor: Richard Lawrence
Time: Friday, Oct 20, Oct 27, Nov 3, 2023 — 10:00AM-4:00PM CT
Location: Blocker 220
Description: This is a three-part course (three Fridays) that covers the core components of Python programming with topics selected to be relevant for research in data science.
Prerequisites: None
ACES: NGS Metagenomics
Instructor: Wesley Brashear
Time: Tuesday, October 24, 2023 — 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: Introduction to Julia
Instructor: Jian Tao
Time: Tuesday, October 24, 2023 — 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: 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
ACES: Introducing Intel PVC GPUs
Instructor: Zhenhua He, Richard Lawrence
Time: Tuesday, November 7, 2023 — 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 computing cluster at Texas A&M High Performance Research Computing, demonstrations of running AI/ML models with the GPUs using PyTorch and Tensorflow, and demonstrations of molecular dynamics using LAMMPS.
Prerequisites: Current ACCESS ID, Unix/Linux skills, basic Python programming skills.
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, November 7, 2023 — 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.
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 Containers (Charliecloud) Technology Lab
Instructor: Richard Lawrence, Zhenhua He, and Wes Brashear
Time: Tuesday, February 14, 2023 — 1:30PM-4:00PM CT
Location: Online using Zoom
Description: This technology lab guides the student though activities to get started with container projects using Charliecloud software suite.
Prerequisites: Current ACCESS ID or HPRC account, Basic Linux/Unix skills, CharlieCloud Tutorial short course or equivalent experience
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: Current 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: Unix/Linux skills; current HPRC account
Fundamentals of R Programming
Instructor: Wesley Brashear
Time: Friday, Apr 21, 2023 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. This course assumes no prior experience with R.
Prerequisites: Unix/Linux skills. Current HPRC account.
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:
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: Technology Lab: Using AI Frameworks in Jupyter Notebook
Instructor: Zhenhua He
Time: Tuesday, November 29, 2022 — 10:00AM-12:30PM CT
Location: Zoom session
Description: This technology lab contains a set of four sessions to help a new user start with his/her machine learning projects on supercomputers at the Texas A&M High Performance Research Computing.
Prerequisites: Current HPRC account, Basic 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 account. 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: Current HPRC account
RNA-seq and Differential Expression
Instructor: Wesley Brashear
Time: Friday, December 2, 2022 — 1:30PM-4:00PM CT
Location: Blocker 220
Description: Covers a brief introduction to RNA-seq technology, NGS QC, and differential expression analysis/data visualization.
Prerequisites: 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: 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: Basic Python skills, HPRC account
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: Current 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: Current 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: Current HPRC account and 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: Current 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: Working knowledge of C/C++ or FORTRAN; Intro to Linux or Unix/Linux skills; Ada account.
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: Working knowledge of C/C++ or FORTRAN; HPRC account.