Orientation: computing resources

Cyberinfrastructure

Throughout the class we will be taking advantage of cyberinfrastructure resources offered by Indiana University and the iPlant Collaborative.

These computing resources are accessed remotely, so students will need to be comfortable connecting to and working on these machines via SSH and VNC. If you are not already comfortable with SSH and VNC, you can find plenty of help resources on the web: for SSH, try a Google search for ssh tutorial windows or ssh tutorial mac; for VNC, the Atmosphere page on iPlant Collaborative's website has a quick tutorial as well as links to additional documentation. Even if you are familiar with VNC, you should still watch the Atmosphere tutorial (linked above) for a brief introduction to iPlant.

The computing resources for this course (particularly the Atmosphere virtual machines) are configured in such a way that you are free to experiment and try new things. You are given full control over your own personal computing environment. If you try to do something on your system and it doesn't work, that's ok. If you mess up your system beyond repair, it's not the end of the world—you simply terminate your system and launch a new one. We don't necessarily expect this to happen to you during the course, nor should you be careless about how you use the class resources. Rather, the point is that you should have the confidence to really immerse yourself in the system, learn how it works, and try new things. If you run into problems or if you're not quite sure how to proceed, you can often find help on the internet in the form of tutorials, question and answer forums, blogs, and more.

If you do run into a problem you can't solve, you are of course welcome to contact the instructors. However, we do insist that you first invest some time exploring your environment, trying things out yourself, and troubleshooting your issues. Some scientific computing skills can be taught, but the most important skills can only be learned and understood by doing.

UNIX command line

Basic experience with the Linux operating system is listed as a prerequisite for this course. Students lacking this experience should have no problem getting up to speed with the basics fairly quickly by going through any number of free tutorials on the internet.

It's not uncommon for scientists without command-line experience to see the terminal as “scary” or foreign. If you are intimidated by the prospect of using the command line, you are not alone. Typing commands is very different from typical laptop or phone usage, where you accomplish tasks by clicking/pressing buttons and where menus provide contextual cues about what a particular program or app can do. But despite any impressions you may have, there is really no need to be intimidated by the command line. With minimal practice you can learn how to work effectively at the command line: list a command's option menu, execute commands, and read terminal messages to determine whether the command ran successfully.

I wrote a short Linux tutorial a few years ago: you're welcome to use this as a starting place, or to search Google for dozens of other Linux command line tutorials. For example, if you search for linux command line tutorial, this page is the first hit…and at first glance it looks like a pretty good tutorial! If you are using Mac OS X, you should be able to complete these exercises using the Terminal application. If you are using Windows, you may consider trying to find a computer lab with Mac or Linux machines available: there should be several in Lindley Hall, for example.

cgss15/orientation/cyberinfrastructure.txt · Last modified: 2015/02/23 10:21 by vbrendel
 
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