Training

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Training Overview

At UF Research Computing we strive to make our resources accessible, efficient, and easy to use. An important part of the effective research computing is the knowledge of how to apply the many available tools in a productive and efficient manner. The comprehensive and clear documentation, well-structured training, and individual help that we provide are all means of achieving that goal. We run a series of training sessions and tutorials during each semester of the school year and in the Summer.

Much of our training content has migrated to the UFIT Training page. The training schedule below is still maintained, though we are in the process of migrating videos to the UFIT page. With the transition to HiPerGator 2.0, much of the content below is out of date and will be removed as new material is placed on the UFIT training page.

You can request a Group Training Session for your group.

Training Schedule


Training Material and Recordings

HiPerGator 2.0 and SLURM training

Introduction to HiPerGator 2.0

HiPerGator 2.0: Moving your research to the next generation of super computing

Writing SLURM Submission Scripts

General Introduction to Research Computing and HiPerGator

An Introduction to the Linux Command Line

This session leads participants through exercises that cover basic Linux commands such as moving around the file system, making directories, moving and copying files, etc. It also overs some of the applications you can use on your computer to connect to and move files to and from HiPerGator.

This session is largely aimed at users who are new to the command line.


Storage at Research Computing

Introducing GatorBox

GatorBox is a Dropbox-like tool for file synchronization and sharing available to Research Computing users. This training introduces the tool and covers basic configuration.

High-Performance Data Transfer with Globus

This training introduces Globus (globus,org) a web-based high-performance data transfer tool available to Research Computing Users.

Application/Discipline Specific Trainings

Galaxy Overview: The Basics

This session focuses on Galaxy, a web-based application platform with the ambitious goal of enabling "data intensive biology for everyone." While Galaxy, and the training, are largely geared toward biology applications, Gaussian, an application for ab-initio molecular electronic structure calculations, is also available through UF Research Computing's Galaxy instance.

This training explores the range of applications available in Galaxy, looking at Blast, next generation sequence analysis, and genome visualization tools. It reviews the data sharing and workflow generation capabilities of Galaxy.

Next Generation Sequencing Data Techniques: Reference-Based Mapping and de Novo Assembly

This training focuses on Next Generation Sequencing (NGS) data. It looks at both reference-based mapping of reads (using Bowtie and Bowtie2) and de novo assembly of reads (using Velvet). I will also briefly highlight some of the other mapping and assembly applications available at Research Computing. We will use both the command line and Galaxy during the demonstration. Users are encouraged to bring their laptop and follow along with some of the analyses.

Next Generation Sequencing Data Techniques: General Methods and Tools

Phylogenetic Analyses

This training covers the basics of running phylogenetic software both in Galaxy and on the command line. We look at resource requests, especially CPU requests for MPI and threaded applications such as MrBayes and RAxML. This training assumes the user is familiar with the applications and is focussed on how to efficiently run the software on the cluster.


MATLAB at Research Computing: A Hands-on Tutorial to Running Your MATLAB Code at Research Computing

This training walks users through a hands-on example of using MATLAB at Research Computing. It looks at using the MATLAB GUI, compiling code and submitting MATLAB jobs to the scheduler to run on the cluster.

UF Research Computing: Overview and Running STATA

This training provides a general overview of Research Computing and an introduction to running STATA on the system. This is geared toward getting STATA users up and running on the cluster.

Advanced Topics

Overview of Programming tools at Research Computing

This session provides an overview of programming tools available at Research Computing, including compilers, debuggers, and performance profiling tools for serial and parallel programs. It covers the basic usage of these tools on Research Computing systems, for example, how to compile parallel programs, find memory leaks and measure performance.


Introduction to GPUs

  • Speaker: Dr. Charles Taylor
  • Download the slides from the presentation.

Course Material

Orientation material for courses using Research Computing

This is the training material presented for courses that wish to use the cluster. See the details of course use of the cluster.

Additional Training Opportunities

In addition to the training sessions coordinated by UF Research Computing, we are aware of many training opportunities provided by other institutions and vendors. These are listed below.


Intel Software Tools Technical Webinar Series

This free webinar series presents tools, tips, and techniques that will help sharpen your development skills on developing and improving your high performance compute applications for multicore and manycore on Intel® Xeon® processors and Intel® Xeon Phi™ coprocessors. Expert technical teams at Intel as well as open source innovators discuss development tools, programming models, vectorization and execution models that will get your development efforts powered up to get the best out of your applications and platforms.

Full schedule and registration information is available here.


XSEDE

The Extreme Science and Engineering Discovery Environment online training mostly lists html tutorials offered at the Cornell University. Offered tutorials cover general programming, scripting, parallel programming (concepts, message passing interface (MPI), openmp), visualisation, code improvement, and other topics.

The XSEDE Training Calendar includes many useful webcasts that are provided by a number of institutions. For most events registration is required.

TACC

Many TACC online training sessions are webcast and are listed in the XSEDE Training Calendar above. Training materials, recordings and webcasts are available from the TACC Course Materials site.

UFRC Historical Training Records

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