Linux environment

1. Linux environment • Graphical interface – X-window + window manager • Text interface – terminal + shell

2. Linux or Mac Desktop • Open up terminal • ssh unid@kingspeak.chpc.utah.edu • ssh –X unid@kingspeak.chpc.utah.edu

3. Windows • Need ssh client • PuTTY • http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html • XShell4 • http://www.netsarang.com/download/down_xsh.html • For X applications also need X-forwarding tool • Xming (use Mesa version as needed for some apps) • http://www.straightrunning.com/XmingNotes/ • Make sure X forwarding enabled in your ssh client

4. New option from all - FastX • Give link to documentation • Good for • Can use to ssh to all interactive nodes – same usage rules apply! • Can also use the frisco{1-6}.chpc.utah.edu nodes for usage beyond that allowed on interactive nodes.

5. Good resources for More Information • Some useful websites http://www.ctssn.com/ http://unix.t-a-y-l-o-r.com/Unix.html”

6. Terminal basics • Two basic shells - slightly different command syntax • csh/tcsh • ksh/bash • Type commands on command line, send command by pressing Enter • Useful key combinations: • ctrl-a – start of line • ctrl-e – end of line • ctrl-c – cancel text typed on line • ctrl-z – put running command to background (come back via command fg)

7. Basic commands • ls – list contents of a directory • pwd – display current directory • cd – change to directory (cd test) • cp – copy file (cp from_file to_file) • mv – move file (mv from_file to_file) • rm – delete file (rm test1) • mkdir – make directory (mkdir test) • rmdir – remove directory (rmdir test) • man – help for given command (man cp)

8. Wildcards • more files can be specified via wildcards • * - matches any number of letters incl. none • ? - matches any single character • [] - encloses set of characters that can match the single given position • - used within [] denotes range of characters • ~ - followed by user name = home directory (~unid) • e.g. - *.csh, figure?.jpg, file[0-9].dat, figure[0-9].*

9. Command flags • commands can take flags that modify their behavior • flags are formed with – (dash) and letter • consult man pages of each command for list of available flags • e.g. • ls -l – list files in long format • rm -r * – remove both files and directories (along with all files in those directories) -- very dangerous!

10. Exercise 1 • Try to make and then cd to a new directory, e.g., IntroLinux1 • List contents of a directory, e.g., /uufs/chpc.utah.edu/common/home/u0028729/CHPCstuff/IntroLunix1 • Try to copy some files from this directory, e.g., to your IntroLinux1 directory • Work with ls, flags, and wildcards • Open man page for some command (e.g. ls) and try some of its flags (e.g. -l, -lt, -ltr)

11. File view commands • cat – display contents of file • more – display contents of file with page breaks (next page with Space key) • head – display top of file • tail – display end of file • grep – search for pattern in file (grep “pattern“ test1) • vi – edit file (more on this later) file – tells you type of file

12. Exercise 2 • View program files via cat, more, head and tail • Vary number of lines viewed with head and tail • Search for a string in a file with grep

13. Command output redirection • > redirect to a new file (cat test1 > test3) • >> - append to a file (cat test2 >> test3) • | - pipe – redirect command output to another command • ls -l | more

14. Exercise 3 • Use cat to concatenate two files • Use pipe, e.g. paginate result of ls

15. Unix File Permissions • Shown with ls -l • User (u), group (g), other (o), all (a) • Permissions are read (r), write (w), execute or search for a directory (x) • chmod – to change permissions of file or directory • Executable and shell scripts must have executable permissions

16. Some other useful commands • wc – e.g. wc -l file.txt • cut – e.g. cut -f 2 -d : file.txt • du – e.g. du -h • df – e.g. df -h • ln – e.g. ln -s ~/bin/prog.exe prog1.exe • Use man pages to find out what these commands do.

17. The vi editor • two modes – command, input • command mode – commands input via keyboard keys • i, a, r, R – enter input mode - insert, append, replace character, replace • G – go to (1G – go to line 1, G – go to end of file) • x, dd – delete character, line • : - enter external command (:w – write file, :q – quit, :q! - quit discarding changes, :wq – write and quit) • /, ? - search forward, backward (/test) • input mode – works like any other text editor

18. Use of the vi editor • to input text, enter input mode • to quit input mode, push Esc key • searching, deleting,... done in command mode • search and replace: :s/old_text/new_text – replace next occurence on current line :s/old_text/new_text/g – replace all occurence on current line :%s/old_text/new_text/g – replace all occurences in the whole file

19. Exercise 4 • Open a file with vi - vi script.csh • Enter edit mode (i) and write text: #/bin/tcsh ls -1 | wc -1 • Exit edit mode (Esc), and save the file (:w). • Oops – we made a typo – last letter is l, not 1. Use replace to fix it. • Save file again and quit (:wq) • Change mode of the script to be able to execute it. chmod u+x script.csh • Practice some more editing with vi