Courses
Last Updated: April 26, 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.
Please make sure you have a valid HPRC account if you want to follow the material by logging in. If you do not have an account, you can apply here.
Registration is required with a classroom seating limit of ~45.
Please bring your own device to follow along during In-Person classes.
Each Short Course runs for 2.5 hours.
Each Primer runs for 1 hour.
For our course offerings from previous semesters, please consult this page.
Short Course List for Spring 2023
Intermediate R Programming
Instructor: Wesley Brashear
Time: Friday, Apr 28, 2023 10:00AM-4:00PM CST (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.
HPRC Primers
Instructor: Aditi Saluja, Abhinand Nasari, Becky Jing, Ashwin Kundeti, Cathleen Li, Ritika Mendjoge, and Amine Sakrout
Time: January 24, 27, and 31, 2023
Location: Online using Zoom
Description: These hour long primers are designed to cover basic topics.
Prerequisites: Current HPRC or ACES account
Introduction to Linux
Instructor: Wes Brashear
Time: Friday, February 3, 2023 10:00AM-12:30PM CST
Location: Blocker 220
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 HPRC account
Introduction to HPRC Computing Resources
Instructor: Lisa Pérez
Time: Friday, February 3, 2023 1:30PM-4:00PM CST
Location: 220 Blocker
Description: Introduction to using HPRC clusters. Policies, hardware overview, getting connected, file systems, computing environment, development environment, batch processing, and common problems.
Prerequisites: Basic Unix/Linux skills; current HPRC account.
Introduction to Composable Resources: ACES and FASTER
Instructor: Lisa Pérez and Dhruv Chakravorty
Time: Tuesday, February 7, 2023 10:00AM-12:30PM CST
Location: Online using Zoom
Description: Introduction to research computing on the composable ACES and FASTER clusters.
Prerequisites: Current ACES account or HPRC account, Basic Linux/Unix skills
Using the Slurm Scheduler on Composable Resources
Instructor: Michael Dickens
Time: Tuesday, February 7, 2023 1:30PM-4:00PM CST
Location: Online using Zoom
Description: Covers various job scheduling approaches using the Slurm Workload Manager on ACES and FASTER.
Prerequisites: Current ACES account or HPRC account
Using Containers on HPRC Resources (Singularity/Apptainer)
Instructor: Richard Lawrence
Time: Friday, February 10, 2023 10:00AM-12:30PM CST
Location: Blocker 220
Description: Covers an overview of container features for the purpose of helping the user determine whether containers are a useful tool for their workflow.
Prerequisites: Basic LINUX/UNIX skills, Familiarity with Slurm, HPRC account. Recommended: Python skills.
Applying for Accounts on HPRC Clusters
Instructor: Sandra Nite and Sheri Stebenne
Time: Friday, February 10, 2023 1:30PM-4:00PM CST
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. There will be a Question and Answer time at the end.
Prerequisites: None
Introduction to Containers (Charliecloud) Tutorial
Instructor: Richard Lawrence, Zhenhua He, and Wes Brashear
Time: Tuesday, February 14, 2023 10:00AM-12:30PM CST
Location: Online using Zoom
Description: This course introduces the use of Containers using the Charliecloud software suite.
Prerequisites: Current ACCESS account or HPRC account, Basic Linux/Unix skills
Introduction to Containers (Charliecloud) Technology Lab
Instructor: Richard Lawrence, Zhenhua He, and Wes Brashear
Time: Tuesday, February 14, 2023 1:30PM-4:00PM CST
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 ACES account or HPRC account, Basic Linux/Unix skills, CharlieCloud Tutorial short course or equivalent experience
Using Matlab on the Grace Cluster
Instructor: Marinus Pennings
Time: Friday, February 17, 2023 10:00AM-12:30PM CST
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, February 17, 2023 1:30PM-4:00PM CST
Location: Blocker 220
Description: We will cover the following commands and topics: vi, sed, awk, grep, Bash Scripting, bc, and customizing your environment.
Prerequisites: Current HPRC account, Basic Linux/UNIX
ACES: Technology Lab: AI Techniques and Usage - Jupyter Notebook
Instructor: Zhenhua He
Time: Tuesday, February 21, 2023 10:00AM-12:30PM CST
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 or FASTER clusters.
Prerequisites: Current ACES account or HPRC account, Python
ACES - Graphcore IPU: Practical Advice for Users
Instructor: Alex Tsyplikhin of Graphcore
Time: Tuesday, February 21, 2023 1:30PM-4:00PM CST
Location: Online using Zoom
Description: Graphcore's Intelligence Processing Units (IPUs) are available in an IPU-POD16 as a part of the ACCESS program at Texas A&M University. This short technical training course provides users with practical advice on how to use IPUs for machine learning and artificial intelligence workloads. The course covers the architecture of the IPU, as well as the use of popular deep learning frameworks such as TensorFlow and PyTorch on the IPU. The course also includes hands-on exercises to give participants a hands-on experience with the IPU and its capabilities.
Prerequisites: Current HPRC account or current ACCESS account. 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, February 24, 2023 10:00AM-12:30PM CST
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, February 24, 2023 1:30PM-4:00PM CST
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
Introduction to Perl
Instructor: Keith Jackson
Time: Tuesday, February 28, 2023 10:00AM-12:30PM CST
Location: Online using Zoom
Description: Covers basic to intermediate level topics with live illustrations and hands-on exercises using the Jupyter notebook web application.
Prerequisites: Current HPRC account
GPU Programming
Instructor: Jian Tao
Time: Tuesday, February 28, 2023 1:30PM-4:00PM CST
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 ACES account or HPRC account, Unix/Linux skills, experience with C or C++
ACES: Clara Parabricks
Instructor: Greg Zynda
Time: Tuesday, Mar 7, 2023 10:00AM-12:30PM CST
Location: online using Zoom
Description: Introduction to Clara Parabricks, a software suite that allows users to perform secondary analysis of next generation sequencing DNA and RNA data. The software incorporated into Clara Parabricks has been optimized to run on GPUs, drastically increasing the speed at which common NGS analyses and tasks can be completed.
Prerequisites: Current ACES account or HPRC account, Unix/Linux skills
ACES: NGS Metagenomics
Instructor: Wesley Brashear
Time: Tuesday, Mar 21, 2023 10:00AM-12:30PM CST
Location: online using Zoom
Description: This short course introduces concepts of metagenomics analysis based on data generated by Next Generation Sequencing (NGS) technology.
Prerequisites: Current ACES account or HPRC account
ACES: Introduction to Julia
Instructor: Jian Tao
Time: Tuesday, Mar 21, 2023 1:30PM-4:00PM CST
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 ACES account or HPRC account
ACES: RNA-seq and Differential Expression
Instructor: Wesley Brashear
Time: Tuesday, Mar 28, 2023 1:30PM-4:00PM CST
Location: online using Zoom
Description: Covers a brief introduction to RNA-seq technology, NGS QC, and differential expression analysis/data visualization.
Prerequisites: Current ACES account or HPRC account
Introductory and Intermediate Python for Data Science
Instructor: Richard Lawrence
Time: Friday, Mar 3, Mar 10, Mar 24, Mar 31, 2023 10:00AM-4:00PM CST
Location: Blocker 220
Description: This is a 4 part course that covers the core components of Python programming with topics selected to be relevant for research in a data science.
Prerequisites: None
Introduction To Short Variant Discovery
Instructor: Wesley Brashear
Time: Friday, Apr 14, 2023 10:00AM-12:30PM CST
Location: Blocker 220
Description: This short course uses example data to complete a standard short variant discovery pipeline, from library QC and trimming, to read mapping, and calling variants using the GATK software suite.
Prerequisites: Unix/Linux skills. Current HPRC account.
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 CST
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.
Fundamentals of R Programming
Instructor: Wesley Brashear
Time: Friday, Apr 21, 2023 10:00AM-4:00PM CST (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.
Intermediate Linux for FASTER/ACES
Instructor: Andrew Palughi
Time: Tuesday, September 27, 2022 10:00AM-12:30PM CST
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 ACES account, Basic Linux/Unix skills
Slurm Job Scheduling
Instructor: Michael Dickens
Time: Friday, September 30, 2022 10:00AM-12:30PM CST
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
Microcredentials in Research Computing
Instructor: Richard Lawrence
Time: Friday, September 30, 2022 1:30PM-4:00PM CDT
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 ACES account or HPRC account
Technology Lab: FEA with moose
Instructor: Andrew Palughi
Time: Tuesday, October 18, 2022 10:00AM-12:30PM CST
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 ACES account 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 CDT and 1:30PM-4:00PM CDT
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 account 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 CST
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 CST
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 account or HPRC account. Basic Linux/Unix skills. C++.
NGS Metagenomics
Instructor: Wesley Brashear
Time: Friday, December 2, 2022 10:0AM-12:30PM CST
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 CST
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 CST
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 CST
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 CST
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 CST
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 CST
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 CST
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.