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The Biomedical Research Computing Facility (BRCF) and the Bioinformatics Consulting Group (BCG) are CBRS core facilities that support local research computing.Note that
Anna's philosophy
Anna is not a Unix guru – there's a world of things she doesn't know! But she knows enough to be considered expert-ish 
. And her knowledge has been hard-won, making many mistakes – even now!
Mistakes are not bad – they're your friend! One of Anna's favorite sayings is:
- Good judgement comes from experience
- Unfortunately, experience comes from bad judgement!
- So go out and start making your first 10,000 mistakes!
Anna's philosophy for teaching Unix is not just to show you how to do thing, but to explain how things work and why. This understanding will greatly help you when you're troubleshooting your own (many!) mistakes. So put on your thinking caps!
About you
Who has had command-line experience before? (E.g. Linux, Unix/Mac Unix, DOS)
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Unix has been around a long time (~1969), before computers had screens or hard drives – magnetic tape and paper tape were used instead. It is written in the C programming language, which was considered a high-level language at the time (– at least compared to assembly language); now . These days C is considered a low-level language .
The original, fundamental "Zen" of Unix is that everything is a file – devices, printers, terminals, and of course actual files.
The GNU project ("Gnu 's is Not Unix") started by Richard Stallman in 1983, provided a lot of open-source tools and utilities to Unix. Popularity of Unix increased dramatically with this development. At this point in time, some Unix flavors were proprietary; others were open or partially open.
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There are many flavors/distributions of Unix, and many flavors/distros distributions of Linux. Some clusters at TACC (the Texas Advanced Computing Center) uses use CentOS, an open-source version of RedHat. Our servers run Ubuntu, from the Debian family of distributionsdistros. Distributions may differ in a number of system management processes, but generally offer a similar set of utilities.
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- Using the command line lets you be very precise and flexible at the same time
- After the initial learning curve (which is non-trivial!!) the command line can be easier – and faster!
- And you You can easily test your command line "mini-scripts" as you develop them
- You can easily work on remote computers from your laptop, as we'll do in this class
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If you choose to follow hands-on, you'll be using the BRCF "GSAF pod", a set of 3 2 compute servers attached to a large, shared storage server.
Accounts and servers
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These credentials are active for the next few weeks, but will be de-activated on Sunday May 12, 2024, in the eveningin mid-May 2025. |
With your studentNN account you can ssh into one of the following servers:
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this server:
- gsafcomp02.ccbb.utexas.edu – even number studentNN accounts
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If you For those associated with UT Austin and are not on the UT campus network, you'll need to have the UT VPN service active in order to connect to these servers via SSH. See How to Connect to the UT VPN Folks not associated with UT Austin, or do not have the UT VPN service installed, can use an alternate web-based method, described below. |
Logging in via SSH
You can access the servers using ssh in a Terminal program that runs on your computer. On Macs, this program is called Terminal. On Windows (Windows 10 or later) it is called Command Prompt or PowerShell. Find and open this program now on your computer.
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# From the UT campus network, or if you have the UT VPN active: ssh student02@gsafcomp02student01@gsafcomp02.ccbb.utexas.edu |
- Answer yes to the SSH security question prompt
- this will only be asked the 1st time you login
- Enter the class password at the password prompt, then press Enter.
- for security reasons, the text that you enter will not be displayed
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If you're using PuTTY as your Terminal from Windows:
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If your Terminal has a dark background, the default shell colors can be hard to read. Execute this line to display directory names in yellow.
We'll see later how to set this environment variable in your login script (~/.profile) so that it gets executed every time you login to this server. For now, just copy the appropriate line above, paste it into your Terminal window (after logging on), then press Enter. |
Logging in via RStudio web
If you're attending remotely and or do not have access to the UT VPN, you can use the Terminal functionality in the RStudio web application.
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To access the Terminal built into RStudio Server.
Click on
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this link: https://
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- Select the RStudio link
- Enter your studentNN account name and our password, then click the Sign In button
- In the RStudio web application, select the Terminal tab above the type-in area
You should now see a command line in the RStudio type-in area.
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In the RStudio Terminal , yellow isif the default color for directories , which can beis difficult to see against its white background . Execute, execute this line to display directory names in blue.
We'll see later how to set this environment variable in your login script (~/.profile) so that it gets executed every time you login to this server. For now, just copy the appropriate line above, paste it into your Terminal window (after logging on), then press Enter. |
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