Use of Hardware

We make a distinction between the lab server, kennicott, which is a powerful computer in the basement of McClure, to which everyone in the group can log in, and also local computers, which might be a desktop or laptop.

An important concept is that different computers, like kennicott, can be operated from a different computer. The address of kennicott, which is accessible while on the University of Idaho campus, is kennicott.ibest.uidaho.edu. If you are off campus, you can make your computer appear to be on campus by using UI’s VPN service. Click here to install UI’s VPN on MacOS or here to install the VPN on Windows. When you are trying to use the VPN off campus, the VPN system will sometimes ask for verification through the DUO Mobile app (via cell phone). Make sure you have access to this.

kennicott can be accessed via a terminal and ssh or as a remote desktop, in which case you can operate kennicott and use kennicott’s fast processors, graphics card, and large amount of RAM. Alternatively, you can mount the kennicott hard drives as a local drive, in which case you can use kennicott’s large amount of data storage and its data backups, but any computing happens on your local desktop or laptop computer, using your personal computer’s processors and memory.

Options for interacting with kennicott include the following:

All require that you be on the university campus, or be using the UIdaho vpn (to appear as though you’re on campus).

Operating as a remote desktop (vnc):

This is likely the most straight-forward, most capable option, and the recommended one if you’re just getting started.

This option uses a web browser to emulate the desktop/gui environment of the linux operating system that runs on kennicott. You can then use a mouse to explore the file system, or open the terminal and interact with the file system through the command line.

In a web browser, navigate to https://kennicott.ibest.uidaho.edu/vnc
Click “Connect” in the center of the page.
From the dropdown menu, choose “Other…”
In the next box, enter your username without the @kennicott… suffix (for example, Chris Miele would enter cmiele).
Enter your password and hit “Log in.”

This will take you to a desktop-style interface with Kennicott. By clicking the black square icon at the bottom (“Terminal Emulator”), you can now access Kennicott through the command line.

Virtual Studio Code (vscode):

Virtual Studio Code is a popular program used for writing and testing different kinds of computer code and it has the ability to access and run files on kennicott. Properly, it can be referred to as an Integrated Development Environment (IDE). VS Code is free software, offered by Microsoft, that can be run on any operating system. Functionality within VS Code, for ssh, jupyter notebooks, etc. is added through “Extensions,” many of which come with a blue check mark to indicate that they are official Microsoft versions. VS Code also offers native integration with git repositories, which make it convenient for working on collaborative projects.

If you install VS Code on your local computer/laptop, and then add the “Remote - SSH” extension from Microsoft, you can log into kennicott and work directly on files on this remote server.

Logging in with a secure shell (ssh):

This option doesn’t handle graphics nearly as well if you’re not physically on campus. However, it involves fewer overhead processes and may be preferable if you have a limited bandwidth connection and only need to operate kennicott textually, with the terminal.

From a Windows machine, you’ll want to use PuTTY (download and install the latest 64-bit MSI). You’ll also want to install and have running XMing. Some instructions for navigating kennicott are given at the bottom of the ‘Files’ page.
From a Mac or Linux computer, open a terminal window (using either terminal or iTerm applications). Then ssh into kennicott by typing ssh -Y USERNAME@kennicott.ibest.uidaho.edu, where USERNAME is your kennicott username. Then enter your password. Some instructions for navigating kennicott are given at the bottom of the ‘Files’ page. From a local mac or linux computer, files can be copied to a different computer that requires an ssh log-in (like kennicott) using rsync (scp also works, but rsync has additional functionality that makes it more desirable for most uses). A typical example might be:
```
 rsync -avzh PATH/TO/WHAT/TO/COPY USERNAME@kennicott.ibest.uidaho.edu:PATH/WHERE/FILE/OR/DIRECTORY/SHOULD/BE/COPIED/
```
Some attention is necessary regarding the use of slashes at the end of the source (WHAT/TO/COPY) path, when using rsync. A slash at the end means copy the directory’s contents. No slash means copy the directory itself, as well as its contents/subdirectories.

Mounting /data/stor as a local drive:

This option allows you to use files stored on kennicott, and then manipulate them on your local computer. Any processing of the files happens with your local computer’s processors and memory.

On a Windows, Mac, or Linux computer, kennicott can be mounted via samba to the local computer filesystem. Then, files can be transferred to and from kennicott’s directories as though it were a local hard drive.

Transfering files using sftp and 3rd party applications:

On a Windows, Mac, or Linux computer, you can manipulate files (copying/moving/renaming/deleting) via some 3rd party applications that use sftp, such as Filezilla on a Windows computer or cyberduck on a Mac.

Talk to Tim about any of the options, or for more information.

Where to do your computing

We do most computing on the group server, kennicott, where we can access each other’s scripts and access shared, group datasets. See the ‘Files’ page on this site for more information and suggestions about how to organize your work.