Getting Started

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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 HiPerGator.png


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, but the passwords are different. 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

To work on HiPerGator you will have to connect to it from your local computer either via SSH (terminal session) or via one of the web/application interfaces we provide such as Galaxy or Matlab (for Matlab distributed computing toolbox pilot project we are testing).

Note about using this guide: for any given command, <username> should be replaced with the UFRC username (same as your GatorLink username).

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

ssh smith@hpg2.rc.ufl.edu

Connecting from 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 <username>@hpg2.rc.ufl.edu
  • Enter your password when prompted. You are now connected and ready to work!

Connecting from Linux

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

Open a terminal and run

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

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

Connecting from MacOS 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 <username>@hpg2.rc.ufl.edu

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

Transferring Data

If you need to transfer datasets to or from HiPerGator and your local computer or another external location you have to pick the appropriate transfer mechanism.

Samba

Samba service, also known as a 'network share' or 'mapped drive' provides you with an ability to connect to some HiPerGator filesystems as locally mapped drives (or mount points on Linux or MacOS X). Once you connected to a share this mechanism provides you with 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 connect to Samba shares.

SFTP

SFTP, or secure file transfer, works well for small to mediaum data transfers and is appropriate for both small and large data files.

If you would like to use a Graphical User Interface ecure file transfer client we recommend:

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.

Rsync

If you prefer to use the command-line or to get maximum efficiency from your data transfers Rsync, which is an incremental file transfer utility that minimizes network usage, is a good choice. It does so by transmitting only the differences between local and remote files rather than transmitting complete files every time a sync is run as SFTP does. Rsync is best used for tasks like synchronizing files stored across multiple subdirectories, or updating large data sets. It works well both for small and large files. See the Rsync page for instructions on using rsync.

GatorBox

UFRC GatorBox service uses the ownCloud storage platform (similar to Dropbox) to provide another option for file management on HiPerGator. GatorBox can be accessed through the web interface (https://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.

Globus

Globus is a high-performance mechanism for file transfer. Globus works especially well for transferring large files or data sets

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.


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 <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.