1. More Unix Naomi Altman

2. Directories Directory = folder mkdir - makes a new directory rmdir - removes an empty directory cd mydirectory - moves you into a directory cd - moves you to "home" pwd - names the current directory. - is the current directory../ - is the directory above the current

3. Environment printenv Prints the settings for your current Unix environment. These can be changed using "set". This is dangerous - you can totally mess up your system by resetting variables in the environment. It is also very useful - e.g. you can set up mail folders, auxillary storage locations, commands. Most of the settings are determined by the files ".cshrc" and ".login"

4. Paths A path is a set of directories to search for commands and files. Generally, you have 2 paths set up - one for commands, programs, etc - one for documentation to be found by "man" echo $path Sometimes you may "lose" a program because it is not in your path. whereis R

5. Adding to your Path set mypath (. usr/local/bin/R) set path ($path $mypath) You can add this to the.cshrc file (using the text editor)

6. File Names Any number of characters and numerals, as well as ".","_" or spaces, but the name should start with a letter. Upper and Lower case are different - i.e. myfile and MyFile are different names. Extensions are not used by Unix, although they may be used by some programs (e.g. Netscape recognizes.htm and.html) or they may be created by some programs (e.g. compilers) Filenames ending in % are meant to be temporary files and may be removed during "clean-up" operations.

7. Wild Cards Many Unix commands recognize "regular expressions". These allow you to search for files or directories, or to find words within files. * matches anything of any length ? matches a single character [x-y] where x and y are numbers or letters matches a single character including x and y and everything that normally falls between them.

8. Matching ls -a ls.g* ls.g[a-c]* ls.g?conf Beware the dreaded rm * (Sad but true): The week before my dissertation draft was due, I ran out of disk space. To remove temporary files I typed rm * % instead of rm *%. OOPS!!! On our system, rm has an "alias" rm -i which asks before removing.

9. Alias Which reminds me that you can make new commands: alias MyCmdName "commands" creates a new command named MyCmdName that executes all the commands in the ""s The new command name will overwrite any Unix command with the same name (so be careful).

10. History history (show command history list) % !! (recall last command) % !-3 (recall third most recent command) % !5 (recall 5th command in list) % !g (recall last command starting with g) % set history=100 Also !!$ is the result of the last function. ls rm !!$

11. Writing Software The make command allows programmers to manage large programs or groups of programs. It aids in developing large programs by keeping track of which portions of the entire program have been changed, compiling only those parts of the program which have changed since the last compile. The make program gets its set of compile rules from a text file called makefile which resides in the same directory as the source files. It contains information on how to compile the software, e.g. the optimization level, whether to include debugging info in the executable. It also contains information on where to install the finished compiled binaries (executables), manual pages, data files, dependent library files, configuration files, etc.

12. Writing Software I can no longer tell you the details of creating a makefile, but it was extremely useful when I was writing c and fortran programs for my dissertation. (These days, that would be c++, java, etc) because it automated the updating process.

13. The Unix Philosophy Unix was written as a toolkit (The LEGO philosophy). The developers provided nails, screws, hammers, etc and expected others to write software. The pieces all fit together - if you don't have the piece you need, you can build it. Because of this, Unix was written for programmers, not users. The user interfaces have been built on top of the toolkit.

14. R and the Unix Philosophy S was a statistical package built to use with Unix. It followed the Unix philosophy. R is a modern version of the original S. When you are running R in Unix, you can execute "shell commands" by proceeding them by ! e.g. ls() is a list of objects in the R workspace !ls is a list of objects in the directory in which you are running R.

15. Why Bother with Unix/Linux Unix was written by a bunch of programmers to facilitate programming. So, it was written to be easy for programmers to extend, which they have. Lots of cool programming tools and environments are available. Unix has much better memory management than Windows, which allows e.g. background computing, and stringing together many CPUs (a cluster) into a supercomputer.

16. Linux Clusters at Penn State http://gears.aset.psu.edu/hpc/systems/