Getting Started

Welcome to UF Research Computing! This page is intended to help new and uninitiated users understand and use UFRC resources. Be sure to check out our training schedule if you'd like help getting started in person!

Overview

The diagram below shown a high-level overview of HiPerGator use. We will go over each part in sections below

Creating an Account

To be able to do anything on HiPerGator you need a UF Research Computing account. Later on we will switch to using GatorLink. At this time we use the same account names that GatorLink uses. To create an account with UF Research Computing, you must read the UFRC Account Policy. After you have reviewed the policy, go to to submit an account request. You will have to tell us the name of the Principal Investigator who sponsors the access of the group. If you are a PI you'll have to indicate it, so we could create a new group for you. Please note that to do useful work your group will have to invest into computational resources or you will have to join a departmental group with a shared allocation.

Connecting to HiPerGator

Note that for any given command, <your_username> should be replaced with the UFRC username (same as your GatorLink username).

For example, if you are referencing the command ssh <your_username>@hpg2.rc.ufl.edu and your Gatorlink username is smith, you would use the command:

ssh smith@hpg2.rc.ufl.edu

Windows

Expand this section to view instructions for logging in with Windows.

Since Microsoft Windows does not come with a built-in SSH client, you must download a client from the web.

UFRC recommends using PuTTY or MobaXterm.

PuTTY

• Download PuTTY to your local machine and start the program
• Configure PuTTY using the configuration instructions for UFRC .
• Select the connection you created in the previous step and click "Open"
• At the login prompt, enter your username (this should be the same as your GatorLink username)
• Enter your password when prompted. You are now connected and ready to work!

MobaXterm

• Download MobaXterm to your local machine and start the program.
• Click "Start local terminal"
• Open a terminal and run ssh <your_username>@hpg2.rc.ufl.edu
• Enter your password when prompted. You are now connected and ready to work!

Linux / Unix

Expand this section to view instructions for logging in with Linux/Unix.

Open a terminal and run

ssh <your_username>@hpg2.rc.ufl.edu

Enter your password when the prompt appears. You are now connected and ready to work!

OS X

Expand this section to view instructions for logging in with OS X.

For OS X users, connection instructions are very similar to those for Linux users.

Terminal, the terminal emulation application for OS X, is located in the folder Applications/Utilities.

Start the Terminal application and run

ssh <your_username>@hpg2.rc.ufl.edu

Enter your password when the prompt appears. You are now connected and ready to work!

Transferring your files

Graphical file transfer client

For many users, a graphical file transfer client is the simplest method of file transfer. UFRC recommends:

• FileZilla (Windows, OS X)
• WinSCP (Windows)
• Cyberduck (OS X)

After you have chosen and downloaded a client, configure the client to connect to sftp.rc.ufl.edu, specifying port number 22. Use your username and password to log in.

GatorBox

GatorBox uses the ownCloud storage platform (similar to Dropbox) to provide a different option for file management. GatorBox can be accessed through the web interface (gatorbox.rc.ufl.edu) or by downloading the ownCloud client. To access storage purchased from UFRC, the user must first set up their UFRC storage as an external storage option within GatorBox.

• See the GatorBox page for more information on this service.
• See the page on adding external storage to GatorBox for detailed instructions on adding your UFRC storage to GatorBox.

Samba

Samba is a file transfer option that allows you to use your client computer's native file manager to access and manage your files. Samba works best for moving smaller files, like job scripts, to and from the system. You must be connected to the UF network (either on-campus or through the VPN) to use Samba.

• See the page on accessing Samba for setup information specific to your computer's operating system.

Globus

Globus is another mechanism for file transfer. Globus works especially well for transferring large files or data sets

• See the Globus page for setup and configuration information.

Rsync

Rsync is a incremental file transfer utility that minimizes network usage. It does so by transmitting only the differences in sequential data, rather than transmitting the complete file. Rsync is best used for tasks like synchronizing files stored across multiple subdirectories, or updating large data sets.

• See the Rsync page for instructions on using rsync.

Editing your files

Several methods exist for editing your files on the cluster.

Native Editors

• vi - The visual editor (vi) is the traditonal Unix editor; however, it is not necessarily the most intuitive editor. View a tutorial for using vi
• emacs - Emacs is a much heavier duty editor, but again has the problem of having commands that are non-intuitive. View a tutorial for using emacs
• pico - While pico is not installed on the system, nano is installed, and is a pico work-a-like.
• nano - Nano has a good bit of on-screen help to make it easier to use.

External Editors

You can also use your favorite file editor on your local machine, and then transfer the files to the cluster afterwards. A caveat to this is that files created on Windows machines usually contain unprintable characters, which may be misinterpreted by Linux command interpreters (shells). If this happens, there is a utility called dos2unix that you can use to convert the text file from DOS/Windows formatting to Linux formatting.

Using installed software

The full list of software available for use can be viewed on the Installed Software page. Access to installed software is provided through Environment Modules.

The following command can be used to browse the full list of available modules, along with short descriptions of the applications they make available:

module spider

To load a module, use the following command:

load module <module_name>

For more information on loading modules to access software, view the page on the basic usage of environment modules.

Running graphical programs

It is possible to run programs that use a graphical user interface (GUI) on the system. However, doing so requires installation of and configuration of additional software on the client computer.

Please see the GUI Programs page for information on running graphical user interface applications at UFRC.

Scheduling jobs using SLURM

UFRC uses the Simple Linux Utility for Resource Management, or SLURM, to allocate resources and schedule jobs. Users can create SLURM job scripts to submit jobs to the system. These scripts can, and should, be modified in order to control several aspects of your job, like resource allocation, email notifications, or output destination.

• See the Annotated SLURM Script for a walk-through of the basic components of a SLURM job script
• See the Sample SLURM Scripts for several SLURM job script examples

To submit a job script from one of login nodes via hpg2.rc.ufl.edu, use the following command:

$ sbatch <your_job_script>

To check the status of submitted jobs, use the following command:

$ squeue -u <your_username>

View SLURM_Commands for more useful SLURM commands.

Getting help

If you are having problems using the UFRC system, please let our staff know by submitting a support request.