UNIX Notes

Our clusters use the Linux Operating System as their core together with some add-on tools provided by the San Diego Super Computing Center.  Together the complete package is known as ROCKS.   Since UNIX is the core of the operating system part of the process of wielding the power of the cluster is learning how use the various UNIX provided, and other commands to manipulate your data.  

There are a number of resources available to help in this process:

• Computer Sciences offers a beginners UNIX course, CS108 (and as well various 1 hour programming classes in C++, Perl, Ruby, Python, etc.  This are all offered under the listing CS105 Programming Languages)
•  The Texas Advanced Computing Center or TACC offers a UNIX class every semester.   (Note:  This is a place holder in case people see this advertised.  As of Feb, 2011 this was not an adequate class).
• O'Reilly and Associates publishes very good books that range from beginner to reference. In particular, Learning the UNIX Operating System is very good.
• Several people have taken courses offered by Perl Source Informatics but they can be pricey.
• Several people have recommended Practical Computing for Biologists
• CCBB is currently working on producing a set of docs to be used in a tutorial session.

There of course may be many other resources that can be located using Google.

Besides learning to use commands, you will at least need to learn some basic shell scripting so that you can write job scripts to submit to the cluster's batch queuing system. The cluster requires those job scripts be written in the syntax of the BASH shell, so our UNIX accounts are created using BASH. You might want to pick up a book on BASH. The O'Reilly and Associates book Learning the BASH Shell is very good.   In the event that you need something more than what we can provide with 3rd party software, you may want to learn to program in a language such as C, C++, or Fortran.  Alternatively, you may want use one of the more advanced UNIX scripting languages such as perl, or python which we install with their add-on modules BioPerl, and BioPython (among others).   Again O'Reilly and Associates is a good source for books on these subjects, as might be the Computer Science classes.   The Department of Statistics and Scientific Computing also offers entry level programming courses.

To use 3rd party software we have added, you will want to learn to use the module command. You can also see the software that we have available on our systems.

Here is a A Little UNIX Dictionary which will let you use many of the buzzwords that you hear.

People that want to run X-Windows (UNIX Graphical User Interface) apps, can read about this on the Using X-Windows at CCBB page.

For more cluster specific information, our Documentation page has a link for Cluster Specific Documentation.

Here is a tutorial showing how to manage disk space in UNIX.