Training

In-Person Training sessions

Research Computing runs regular in-person training sessions throughout the year. These sessions are free and open to all UF researchers. Most sessions include hands-on exercises and users are encouraged to bring their own computers.

In addition to the regularly scheduled sessions, you can request a Group Training Session for your group.

Many of the sessions are also available as pre-recorded videos linked from this page and also listed on the UFIT Training page.

Quick Help Videos

The following videos are designed to provide quick help for users on various topics. Most are only a few minutes long.

Please let us know if there are additional topics that you feel would be useful for a quick help video.

Connecting to HiPerGator

ssh from MacOS

[2 min, 22 sec] This video demonstrates launching the MacOS Terminal, logging into HiPerGator at hpg.rc.ufl.edu using ssh, and demonstration of the user's /home and /ufrc directories.

• The HiPerGator hostname is: hpg.rc.ufl.edu
• Your username and password are your Gatorlink username and password.

ssh from Windows

[3 min, 41 sec] This video covers download and installation of the Windows ssh client MobaXterm, logging into HiPerGator at hpg.rc.ufl.edu using ssh, demonstration of /home and /ufrc directories and copy/paste on Windows ssh clients.

• The HiPerGator hostname is: hpg.rc.ufl.edu
• Your username and password are your Gatorlink username and password.

Using Jupyter Notebooks on HiPerGator

[8 min, 1 sec] This video covers the use of Jupyter Notebooks via https://jhub.rc.ufl.edu/ to run Python, R and other notebooks on HiPerGator.

• Connect to https://jhub.rc.ufl.edu/
• Launch notebooks in various coding languages
• Launch a terminal
• Upload and download files via your browser

Using Open on Demand on HiPerGator

[5 min, 11 sec] This video covers the use of Open on Demand https://openondemand.org/ on HiPerGator via https://ood.rc.ufl.edu/.

• Connect to https://ood.rc.ufl.edu/
• Launch a terminal
• Launch many graphical applications like Rstudio, Matlab and Freeview
• Manage job submission
• Upload, download and edit files via your browser

Data Transfer

SFTP transfer with FileZilla

[2 min, 12 sec] This video demonstrates using the FileZilla SFTP client to transfer data to/from HiPerGator.

• The HiPerGator hostname is: hpg.rc.ufl.edu
• note: for larger transfers, you may have better network performance with the host: sftp.rc.ufl.edu
• Your username and password are your Gatorlink username and password.
• The port for SFTP transfers is: 22

Data transfer with Globus

[4 min, 22 sec]

This video demonstrates the basics of:

• Logging in to Globus.org using UF Gatorlink credentials.
• Connecting to the UFRC main endpoint at ufrc#hpg2
• Connecting to another endpoint for data transfer
• Transferring a file
• Additional options for file transfer, including folder synchronization and encryption.

View Globus page for overview.

Setting up Globus Connect Personal

[3 min, 24 sec]

This video demonstrates the basics of:

• Establishing a Globus Connect Endpoint for your computer
• Installing the Globus Connect Personal client
• Using the setup key to initialize your client.

Setting up a shared end-point with Globus

[3 min, 42 sec]

This video demonstrates the basics of:

• Connecting to the ufrc#hpg2 endpoint
• Designating a folder as a shared endpoint
• Setting share options
• Creating a Globus group

View Globus page for overview.

Data transfer with Samba

View Samba page for overview.

Samba Access from MacOS

[2 min, 46 sec] This video demonstrate how to mount a UFRC filesystem on your MacOS computer using Samba.

Samba Access from Windows

[2 min, 1 sec] This video demonstrate how to mount a UFRC filesystem on your Windows computer using Samba.

Storage and Data Management

Restoring Files in /home from snapshots

[5 min, 43 sec]

A small home directory (20GB quota) is provided for HiPerGator users, which is not intended for high performance work. Your /home area is intended for source code, scripts, and other human-readable data; the amount of data stored in your /home area should be kept to a minimum. Home directories have one week of daily snapshots available, which can be accessed by the user to recover older versions of files or accidentally deleted files. This video shows how to restore these files.

Submitting Jobs

Running many short jobs with job arrays

[10 min, 16sec] This video reviews important considerations for running SLURM Job Arrays, especially when the individual tasks are short in duration. The video walks through the example script on the Job array page to help users run multiple short tasks in a single job to maximize their efficiency.

Making Investments in UF Research Computing Resources

Submitting a purchase request

[3 min, 34 sec]

This video covers:

• UFRC Price sheets
• Hardware vs. Services investments
• Submitting the purchase request form

Training Videos

In addition to the in-person training sessions, we provide pre-recorded content for many of our sessions.

Introduction to Research Computing and HiPerGator

Intended for new users, this training provides a general overview of the UF Research Computing facilities and basic usage of HiPerGator.

This training is available as a three-part series on the UFIT Training site:

Or as a recording of the most recent Zoom session:

Recording of the Sept. 10, 2020 session. I apologize that the first minute was not captured in the recording.

You can download a copy of the slides used from here.

Introduction to the Linux Command Line

This session will lead participants through some exercises that go over basic Linux commands such as moving around the file system, making directories, moving and copying files, etc. We will also go over 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.

The handout and files for the session are now located in a git repository here: https://github.com/UFResearchComputing/Linux_training

The handout can be downloaded as a PDF file.

The molecules folder used in the training is at /data/training/LinuxCLI/molecules.

For those wishing to use this training outside of HiPerGator, the molecules folder is part of the Software Carpentry Unix Shell training available in the data-shell.zip file on the setup page. This can be downloaded to you own computer and run using the Mac/Linux Terminal or MobaXterm terminal on Windows.

HiPerGator: SLURM Submission Scripts

In this session, participants will practice working with SLURM submission scripts using sample files. The training will cover the most common scheduler directives and how to tell SLURM the information it needs to run your jobs efficiently. Example scripts will be provided, though users are encouraged to bring their own scripts to work with. This session assumes a basic familiarity with the Unix command line and will be aimed at beginning to intermediate users. See the Introduction to the Linux Command Line Training for help with Linux.

This video is approximately 30 minutes and includes a demonstration.

The files used in this video are on the Sample_SLURM_Scripts page and on the cluster in /ufrc/data/training/SLURM/.

HiPerGator: SLURM Submission Scripts for MPI Jobs

This session will go into depth on the details of scheduling MPI jobs on HiPerGator. Efficiently running MPI applications requires an understanding of both how to specify the needed resources as well as the layout and properties of the available hardware. This session will provide examples from several commonly used applications and provide guidelines for users to optimize their own runs.

This video is approximately 26 minutes and includes a demonstration.

The files used in this video are on the Sample_SLURM_Scripts page and on the cluster in /ufrc/data/training/SLURM/.

Running Graphical Applications on HiPerGator with Xpra

Users can run applications with graphical user interfaces (GUI) on HiPerGator in the SLURM “gui” partition. Xpra is the software we use to connect to the graphics window of the application running on HiPerGator from your local computer. These videos walk through setting up and connecting to Xpra sessions.

The new gui/2 module is explained in this video: [5 min, 16 sec]

Also check out the Open on Demand video which covers many GUI applications: [5 min, 11 sec]

For the older, gui/1 modules, there are both Mac and Windows versions are available and are about 10 minutes each:

The GUI Programs page has additional information.

Running MATLAB on HiPerGator

Users walk through a hands-on examples using MATLAB at Research Computing. Participants will work with the MATLAB GUI, compiling code and submitting MATLAB jobs to the scheduler to run on the cluster.

This video is approximately 24 minutes and includes a demonstration.

Users should also review the Matlab page for additional information.

Git and GitHub.com

While there is not a video associated with this, all of the content is available online.

• Slides for the presentation are at: https://ufresearchcomputing.github.io/git-training/#/
• The hands-on content is in the master branch of the repository at: https://github.com/UFResearchComputing/git-training

Orientation Material for Courses using HiPerGator

For UF courses that use HiPerGator, please review our policies on teaching use of HiPerGator.

Recordings and slides are on the UFIT Training page:

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.