Short Courses

Last Updated: October 16, 2017

Every semester, HPRC holds short courses ranging in topics for beginning, intermediate, and advanced users. Every semester we start with the Introduction to Unix/Linux course. It covers material that is prerequisite to ALL other short courses. This, along with the Introduction to Using the Ada Cluster and Introduction to Using the Terra Cluster 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.

Short Course List for Fall 2017

Introduction to Code Parallelization using OpenMP

Times: Tuesday, October 17, 2:30p - 3:55pm

Description: Covers code parallelization for shared memory systems using the OpenMP standard of directives and calls.

Prerequisites: Unix/Linux skills (covered in the Intro to Unix/Linux course) and a working knowledge of C/C++ or FORTRAN; Ada account.

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RNA Sequencing

Times: Wednesday, October 18, 1:00pm - 3:00pm

Description: Covers concepts of RNA-seq analysis for transcriptome assembly, differential expression and variant calling.

Prerequisites: Unix/Linux skills; Ada account; the Introduction to Next Generation Sequencing course.

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Python for MATLAB Users

Times: Thursday, October 19, 2:30p - 3:55pm

Description: Introduces Python from the perspective of a MATLAB user. The basics of Python programming language will be covered.

Prerequisites: Intro to MATLAB short course or experience with MATLAB.

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Introduction to Code Parallelization using MPI (Part I)

Times: Tuesday, October 24, 2:30p - 3:55pm

Description: Covers basic concepts in MPI, including distributed memory systems, messages, blocking/non-blocking, point-to-point communication, collective communication.

Prerequisites: Unix/Linux skills, the Intro. to Ada course, and a working knowledge of C/C++ or FORTRAN; Ada account.

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NGS Assembly

Times: Wednesday, October 25, 1:00pm - 3:00pm

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

Prerequisites: Unix/Linux skills; Ada account; the Introduction to Next Generation Sequencing course.

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Introduction to Code Parallelization using MPI (Part II)

Times: Thursday, October 26, 2:30pm - 3:55pm

Description: Covers self-scheduling, task and data distribution, domain decomposition, MPI/OMP hybrid programming

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Intermediate CUDA Programming

Times: Tuesday, October 31, 2:30pm - 3:55pm

Description: Covers some intermediate topics in CUDA programming on NVIDIA GPUs. Topics include GPU memory management, parallel kernels in CUDA C. profiling and performance evaluation, etc..

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 CUDA course; Intro to Ada course, if Ada account is required.

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NGS Metagenomics

Times: Wednesday, November 1, 1:00pm - 3:00pm

Description: Covers concepts of metagenomics analysis.

Prerequisites: Unix/Linux skills; Ada account; the Introduction to Next Generation Sequencing course.

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Introduction to CUDA

Times: Thursday, November 2, 2:30p - 3:55pm

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; Intro to Ada course; Ada account.

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Introduction to Terra: Atomistic Simulations (Quantum Software)

Times: Tuesday, November 7, 2:30p - 3:55p

Description: Covers a variety of topics relevant to quantum atomistic simulation software installed on Terra. The course will include a lecture and live demonstrations by the instructor.

Prerequisites: None

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Introduction to HPRC Galaxy

Times: Wednesday, November 8, 1:00pm - 3:00pm

Description: Covers usage and best practices for the HPRC Galaxy.

Prerequisites: Ada account.

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Introduction to Terra: Atomistic Simulations (Classical Software)

Times: Thursday, November 9, 2:30pm - 3:55pm

Description: Covers a variety of topics relevant to classical atomistic simulation software installed on Terra. The course will include a lecture and live demonstrations by the instructor.

Prerequisites: None

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Introduction to Ada: Atomistic Simulations (Quantum Software)

Times: Tuesday, November 28, 2:30p - 3:55p

Description: Covers a variety of topics relevant to quantum atomistic simulation software installed on Ada. The course will include a lecture and live demonstrations by the instructor.

Prerequisites: None

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NGS RADSeq/GBS

Times: Wednesday, November 29, 1:00pm – 2:55pm

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

Prerequisites: Basic Unix/Linux skills. Ada account.

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Introduction to Fortran on Ada and Terra

Times: Thursday, November 30, 2:30p - 3:55pm

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: Basic Unix/Linux skills. Ada or Terra account.

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Introduction to Databases

Times: Tuesday, December 5, 2:30p - 3:55pm

Description: Covers SQLite, the most widely used relational database. Topics include: command line tools to manage SQLite databases and files (CSV and TXT files), Structured Query Language (SQL) to manage relational databases including SQLite, and tool sqliteman with graphical user interface to operate on SQLite databases.

Prerequisites: Ada or Terra account.

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Introduction to Ada: Atomistic Simulations (Classical Software)

Times: Thursday, December 7, 2:30pm - 3:55pm

Description: Covers a variety of topics relevant to classical atomistic simulation software installed on Ada. The course will include a lecture and live demonstrations by the instructor.

Prerequisites: None

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