Short Courses

Last Updated: September 12, 2019

Every semester, HPRC holds short courses ranging in topics for beginning, intermediate, and advanced users. Every semester we start with the Introduction to Linux course. It covers material that is prerequisite to ALL other short courses. This, along with the Introduction to the Ada and Terra Clusters course form the absolute minimum basis for using the respective clusters effectively. All courses will be delivered in an interactive style through a live login session. Attendants can bring laptops although installed workstations will be available. 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.

Each short course is a one day course. Registration is required with a seating limit of ~45.

For our course offerings from previous semesters, please consult this page.

Short Course List for Fall 2019

Introduction to the Ada and Terra Clusters

Instructor: Mark Huang, Michael Dickens

Time:

  • Friday, September 6, 1:30PM-4:00PM
  • Friday, September 13, 10:00AM-12:30PM

Location: SCC 102.B

Description: Covers a variety of topics relevant to computing on the Ada and Terra clusters, demonstrated through a live login session. The topics include, but are not limited to, basic system information, compiling and running programs, as well as batch processing. Use of the batch system will be demonstrated with real-time examples. Each session covers material for BOTH clusters.

Prerequisites: Unix/Linux skills; Ada account.

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Data Management Practices

Instructor: Dylan Rodriguez

Time: Friday, September 13, 1:30PM-4:00PM

Location: SCC 102.B

Description: Explore the basics of storing, organizing, finding, managing, moving and munging the data you use in your research.

Prerequisites: None

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Introduction to Python

Instructor: TBD

Time: Friday, September 20, 10:00AM-12:30PM

Location: SCC 102.B

Description: Covers basic topics in programming using Python. Topics include variables, data types, control statements, functions, I/O, modules, interactive execution of python statements, python scripts, dictionaries, sorting, and regular expressions.

Prerequisites: None

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Introduction to Scientific Python

Instructor: TBD

Time: Friday, September 20, 1:30PM-4:00PM

Location: SCC 102.B

Description: This short course covers several topics and packages for scientific programming in Python.

Prerequisites: Intro to Python course or basic Python knowledge

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Linux Workshop

Instructor(s): Lisa Perez

Lecture: Friday, September 20, 6-8:45PM, Chemistry (CHAN), Room 2104

Hands-on Sessions:

Lab Session (Rm. 2109 Chemistry): Monday, September 23, 9AM-12PM
Lab Session (Rm. 2109 Chemistry): Monday, September 23, 2-5PM
Lab Session (Rm. 2109 Chemistry): Tuesday, September 24, 9AM-12PM
Lab Session (Rm. 2109 Chemistry): Tuesday, September 24, 2-5PM

Description: The Linux workshop is designed to teach a user the basic commands necessary to work in a Linux environment and consists of a 2 hour 45 minute lecture, and a 3 hour hands-on exercise session. This workshop is normally offered once during the Fall, Spring, and Summer sessions.

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NOTE: You must be on-campus or use VPN to access the registration page.

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Introduction to Next Generation Sequencing

Instructor: Michael Dickens

Time: Tuesday, September 24, 9:30AM-12:00PM

Location: WCL 126

Description: Covers concepts of sequence mapping, variant calling and ChIP-seq analysis utilizing tools available on the Ada cluster.

Prerequisites: None

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NGS Assembly

Instructor: Noushin Ghaffari

Time: Tuesday, October 1, 9:30AM-12:00PM

Location: WCL 126

Description: Covers concepts of genome assembly using Next Generation Sequencing (NGS) technology. An assembly example will be covered during class using sample data.

Prerequisites: Ada account

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Introduction to Fortran

Instructor: Jian Tao

Time: Friday, October 4, 10:00AM-12:30PM

Location: SCC 102.B

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: None

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Introduction to Julia

Instructor: Jian Tao

Time: Friday, October 4, 1:30PM-4:00PM

Location: SCC 102.B

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: None

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NGS Metagenomics

Instructor: Noushin Ghaffari

Time: Tuesday, October 08, 9:30AM-12:00PM

Location: WCL 126

Description: Covers concepts of metagenomics analysis.

Prerequisites: Ada account

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Introduction to the MATLAB Parallel Toolbox

Instructor: Marinus Pennings

Time: Friday, October 11, 1:30PM-4:00PM

Location: SCC 102.B

Description: This MATLAB course will introduce the MATLAB parallel toolbox. Topics discussed include cluster profiles, parallel pools, parfor, spmd, distributed data, and GPU computing. We will also demonstrate how to run parallel MATLAB jobs on the HPRC clusters.

Prerequisites: Basic MATLAB skills. Ada account

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Molecular Modeling Workshop

Instructor(s): Lisa Perez

Lecture Times (Rm. 2104 Chemistry): Friday, October 11, 6-9PM

Lab Sessions:

Lab Session (Rm. 2109 Chemistry): Monday, October 14, 9AM-12PM
Lab Session (Rm. 2109 Chemistry): Monday, October 14, 2-5PM
Lab Session (Rm. 2109 Chemistry): Tuesday, October 15, 9AM-12PM
Lab Session (Rm. 2109 Chemistry): Tuesday, October 15, 2-5PM

Description: The molecular modeling workshop is designed to teach a user the fundamental principles and concepts of molecular modeling with an emphasis on molecular mechanics/dynamics. Who should attend: Researchers and students that are interested in learning how molecular modeling can be utilized to investigate chemical properties to steer experimental research and/or enhance the understanding of experimental results. The molecular modeling workshop consists of a 3 hour lecture with a 15 minute break and a 3 hour hands-on exercise session.

Prerequisites: Linux Workshop or a working knowledge of Linux.

NOTE: You must be on-campus or use VPN to access the registration page.

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NGS RADSeq/GBS

Instructor: Shichen Wang

Time: Tuesday, October 15, 9:30AM-12:00PM

Location: WCL 126

Description: Covers concepts of RADseq/GBS experimental design and data analysis.

Prerequisites: Ada account

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Introduction to Perl

Instructor: Keith Jackson

Time: Friday, October 18, 1:30PM-4:00PM

Location: SCC 102.B

Description: Covers basic to intermediate level topics with live illustrations and hands-on exercises using the Jupyter notebook web application.

Prerequisites: None

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Introduction to R

Instructor: Noushin Ghaffari

Time: Friday, October 25, 10:00AM-12:30PM

Location: ILSB Auditorium

Description: This course aims at introducing R as a software environment for statistical computing.

Prerequisites: Unix/Linux skills. Ada account.

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SLURM Job Scheduling

Instructor: Michael Dickens

Time: Friday, October 25, 1:30PM-4:00PM

Location: SCC 102.B

Description: Covers various job scheduling topics such as tamulauncher, job arrays, etc. using SLURM on the Terra cluster.

Prerequisites: None

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Introduction to Deep Learning with TensorFlow

Instructor: Jian Tao

Time: Friday, November 1, 10:00AM-12:30PM

Location: SCC 102.B

Description: Covers using TensorFlow for deep learning.

Prerequisites: Experience with Python

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Introduction to CUDA

Instructor: Jian Tao

Time: Friday, November 1, 1:30PM-4:00PM

Location: SCC 102.B

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: Unix/Linux skills; Experience with C or C++; Ada account is required for those who do not have access to a machine that can execute CUDA code; Intro to Ada course, if Ada account is required.

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Introduction to Code Parallelization using OpenMP

Instructor: Marinus Pennings

Time: Friday, November 08, 10:00AM-12:30PM

Location: SCC 102.B

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.

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Introduction to Code Parallelization using MPI

Instructor: Marinus Pennings

Time: Friday, November 08, 1:30PM-4:00PM

Location: SCC 102.B

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; Ada account.

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