HiPerGator cota-dept Onboarding

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HiPerGator cota-dept Onboarding

#1 Post by jstenner »


Welcome to the UF College of the Arts HiPerGator Account!

If you are new to HiPerGator, your first step is to watch the Coursera New User Training linked here:

Next, watch the pre-recorded training videos (Part 1-3) at the following link:

Below are basic instructions for initial setup that will allow your account to be configured in a way that complies with the needs of UF Research Computing. It distills information provided on UFRC Help and Documentation regarding the initial setup. Complete help can be found here:

If you aren't familiar with how to utilize the command line, you may want to watch this tutorial (free via UF):
Learning Linux Command Line

Requesting an Account

Go here to request a HiPerGator account:
https://www.rc.ufl.edu/get-started/hipe ... r-account/

Select “Haring, Pete” as faculty sponsor from the drop-down list and complete the rest of the form. In the “Comments” box type, “Please also add me to the cota-dept secondary group.” You will receive an email with instructions on required training, etc.

Once your account is approved, you can log into HiPerGator using your operating systems Terminal program to initiate a secure shell (SSH) connection. Substitute your username for <username> below:
Screen Shot 2022-05-04 at 8.21.38 AM.png
You will be prompted to select your preferred multi-factor authentication mechanism:
Screen Shot 2022-05-04 at 8.34.00 AM.png
Once you’ve authenticated your shell session will begin:
Screen Shot 2022-05-04 at 8.34.44 AM.png

Sharing Files with Group

Once your account is approved, there are some configuration items you'll likely want to implement. If you're working with a graduate student, for example, you'll need to be able to view and work with each other's files. If you add ”umask 007” to your .bashrc or .bash_profile, this will allow all new files created to be visible to members of the cota-dept user group.

Details here:

You can use the Linux text editor “nano” to edit this configuration file which is located in your home (~) directory:
Screen Shot 2022-05-04 at 8.49.14 AM.png
After pressing “enter” the text editor will display the contents of .bash_profile. Yours will likely look different than mine, but the blue highlighted text “umask 007” below is what you need to add. You can enter any comment you like after the # symbol. Comments are good to remind you what various entries do/provide, etc:
Screen Shot 2022-05-04 at 8.46.23 AM.png

Now, type Control + o to “WriteOut” your changes (i.e. to save your changes to file), then press Enter. Notice the keyboard commands are conveniently displayed on the bottom two lines of the editor interface. If you’ve done it correctly it will tell you how many lines were written to file. Type Control + x to exit the editor you will be returned to the shell.

In order to make the changes apply to your current shell session, you can either log out and back in, or you can run the following command:
Screen Shot 2022-05-04 at 9.15.10 AM.png
From now on, any new files or directories you create can be accessed by members of the group: cota-dept.

Create a Working Directory

As described in the HiPerGator training, you will want to store your working files on “blue” rather than your home directory. To configure this, create a working directory with your login shortname <gatorusername> in /blue/cota-dept/<insertdept>/

For example, if my <gatorusername> is “stenner” and I am part of the School of Art + Art History, I would create a subdirectory called stenner in /blue/cota-dept/saah/ using the “mkdir” command. Substitute your username for <gatorusername> below:
Screen Shot 2022-05-04 at 9.29.59 AM.png

If you want to, you can create a symbolic link (i.e. a shortcut) to this path in your home area so you don’t have to remember the full path to your working directory. Google “Linux symbolic link”.

Configure Anaconda

Anaconda or “conda” is commonly used to configure and install libraries and packages needed for AI work. These files can be large, so again, you don’t want to fill up your home area, right? The solution is to configure Anaconda to install its files to your new working directory, instead. To do so, you'll need to modify the Anaconda configuration file that is stored in your home area. This file is called ".condarc" and it needs to point to your new working directory. The first time you log in, this file will not exist. You can create it manually, or, better yet, it can be created by using HiPerGator’s module system. At the command prompt, type: “module load conda”
Screen Shot 2022-05-04 at 9.47.27 AM.png
You can check to see that it has loaded the latest version of Anaconda by typing “module list” (see above). By loading the module, a basic .condarc file will be created in your home directory.

Now, navigate to your home directory and edit the config file:
Screen Shot 2022-05-04 at 9.50.48 AM.png

If this is your first time using HiPerGator, add the following lines highlighted in blue to your .condarc file. Be sure to substitute your department (sotd, som, etc.) for “saah” below if you’re not in saah. As we did previously, type Ctrl + o to WriteOut the changes and Ctrl + x to exit:
Screen Shot 2022-05-04 at 9.52.21 AM.png

If you have done this before as part of a class allocation, REPLACE those entries with these. The paths shown in the graphic above should be modified to point to the directory where you'd like conda package files to be stored. For example, if you're taking ART4630, you'll replace "cota-dept/saah" with "art4630".

This ensures that all your conda environments and package installs are placed on BLUE and in your working directory rather than in your login node, "home" directory, as requested in the HiPerGator training video. This information, with more detail, is documented at:


That’s it. You should be good to start working!
The master of disaster!

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