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- Anna Battenhouse, Associate Research Scientist, abattenhouse@utexas.edu
- BA English literature, 1978, Carleton College
- Commercial software development 1982 – 2007
- Texas Instruments, Motorola ...
- lots of software development experience but limited Unix/Linux
- Joined Vishwanath Iyer Lab 2007 (functional genomics)
- “retirement career”
- began to appreciate Linux & bash (slowly)
- BS Biochemistry, 2013, UT
- Current affiliations:
- Manager, Biomedical Research Computing Facility (BRCF)
- member, Bioinformatics Consulting Group (BCG)
- member, Marcotte lab (systems biology/proteomics)
The Biomedical Research Computing Facility (BRCF) and the Bioinformatics Consulting Group (BCG) are CBRS core facilities that support local research computing.
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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 
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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. Severak 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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Why not use a program with a GUI (Graphical User Interface) instead?
- Programming involves writing files anyway, and is constrained by the language environment used
- 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 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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These credentials are active for the next few daysweeks, but will be de-activated on Sunday November 19, 2023 in the morningat the end of November 2024. |
With your studentNN account you can ssh into one of the following servers:
- gsafcomp01.ccbb.utexas.edu – odd number studentNN accounts
- 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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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 one of these links:
- 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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export LS_COLORS=$LS_COLORS:'di=1;33:fi=01:ln=01;36' |
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export LS_COLORS=$LS_COLORS:'di=1;34:fi=01:ln=01;36:' |
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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