June Workshop Setup

Please follow the instructions below to ensure your computer is setup and ready for the workshop.

If you have any difficulties with any of the steps, please contact us at hcc-support@unl.edu or visit us in person at our offices:

  • Lincoln: Room 118 in the Schorr Center at UNL's City Campus
  • Omaha: Room 152 in the Peter Kiewit Institute at UNO's Scott Campus

June 5: Connecting to HCC Clusters and Introduction to Bash
June 12: Introduction to Bash (cont.) and Revision Control with Git
June 19: Submitting Jobs and Handling Data on Crane
June 26: Anvil: HCC's Cloud and the Open Science Grid

Return to the Workshop Page
June 5: Setup Accounts and SSH Client

For the workshop this week, you will need an HCC account. If you do not currently have one, you can request one by completing a new user request form.

Please note that all new accounts must be associated with an established HCC group. If your research group is not currently established with HCC, the group PI must first complete a new group request form. Once the group has been setup, you may then request a new user account. For those who do not have a group to request an account under and are unable to create a group, demo accounts will be provided for use during the workshop.

To connect to the Holland clusters, we will use an SSH client. SSH stands for Secure SHell and is the protocol used to connect securely to a remote computer. To install an SSH client, please follow the directions below.

Windows Mac OS X Linux

For Windows, we recommend the PuTTY Client. To install PuTTY, download the PuTTY Package file appropriate for your machine and double click the file to run it. Follow the onscreen prompts, accepting the default settings provided.

All versions of Mac OS X come with Terminal, which has SSH capabilities. To open the terminal on OS X, open your Applications folder, then open the Utilities folder. Open the Terminal application. You can also launch the terminal by using Spotlight search in OS X and searching for “terminal”. You may want to keep Terminal in your dock for this workshop.

Most flavors of Linux come with a built in terminal or with XTerm preinstalled. There is no need to install anything extra.


June 12: GitHub Account

If you did not attend the June 5th class, please ensure you have an active HCC account by following the directions above.

Git is a version control system that lets you track who made changes to what and when, and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.


June 19: Install Globus Connect

If you have not attended either of the previous sessions, please ensure you have an active HCC account by following the directions above.

We will be using Globus Connect to transfer files to and from the clusters. Please set up an account by visiting the Globus website and clicking the "Login In" button. Individuals from UNL, UNMC, and UNK can login using their institutional credentials, otherwise you can set up a Globus ID to use for login.

After successfully logging in, please set up a Globus Connect Personal Endpoint on your personal machine by following the directions below which correspond to your operating system.

Windows Mac OS X Linux

Detailed installation information for Windows can be found on the Globus website.

Detailed installation information for Mac OS X can be found on the Globus website.

Detailed installation information for Linux can be found on the Globus website.


June 26: Install Anvil Clients

If you have not attended either of the previous sessions, please ensure you have an active HCC account by following the directions above.

HCC's cloud resource, Anvil offers virtual machines that are ideal for applications not suited to the traditional Linux command line environment. To connect to virutal machines on Anvil, we will need to use a VPN client.

If you have login information for the UNL, UNO or UNK VPN, you can or may already have installed the Cisco AnyConnect Client. This will be sufficent for our workshop. If you do not have access to any of these VPNs, please follow the directions below to install OpenConnect

Windows Mac OS X Linux

Download OpenConnect GUI and install by following onscreen prompts, ensuring that "Do not add openconnect-gui to the system PATH" is selected on the appropriate screen.

Download OpenConnect GUI. After extracting, you can run the application by running "OpenConnect-GUI".

To install OpenConnect on Linux, open a terminal and type `yum install openconnect` or `apt-get install openconnect` depending on your distrubtion of Linux.

To connect to an Anvil virtual machine, we will use a remote desktop client (to connect to Windows instances) and an SSH client (to connect to Linux instances). Please follow the directions below to ensure you have the correct clients installed.

Windows Mac OS X Linux

If you attended any of the previous sessions, you should already have an SSH client installed, if not, please follow the directions above to install PuTTY on your system.

Windows comes with Remote Desktop by default. No additional installation is necessary.

Remote Desktop client is available on iTunes for free. Please download the client and install by following on screen prompts.

Mac users can use the built in Terminal for an SSH client. No additional installation is necessary.

Remmina or rdesktop are both Remote Desktop clients available for Linux. To install Remmina, open the Terminal and enter the command `yum install remmina` or `apt-get install remmina` depending on your distribution of Linux.

Linux users can use the built in Terminal for an SSH client. No additional installation is necessary.