1. Introduction to Advanced UNIX
March
Kevin Keay

2. Outline Overview Resources The basic form of a typical C-shell script
Introduction to C-Shell Programming
Advanced UNIX materials: The following are PDF documents that may be used for reference but won’t be discussed in detail during this short course:
Part 1 : Scripts
Part 2 : A summary of useful software
Part 3 : Reanalysis products
Lab session (informal) 2-3:30 PM UNIX Lab
See:

3. Overview
This is a practical course that is designed to give you the basic skills to write UNIX C-shell scripts
You can only truly understand the concepts by putting them into practice!

4. Overview (2) We will look at the basic form of a C-shell script
There will be a quick tour through Introduction to C-Shell Programming
There are some extra advanced UNIX materials (Parts 1-3) that you may need to reference. Some aspects will be looked at during the lab session but they are intended for personal reference
Part 1 covers C-shell scripts and some additional concepts
Part 2 is a summary of some useful software
Part 3 focuses on downloading and decoding reanalysis data (NetCDF and GRIB)
Finally, there is a short Lab session

5. Resources
A very useful and concise reference book covering UNIX and the C shell is:
UNIX in a Nutshell, O’Reilly and Associates (Engineering Library: GILL).
A useful online resource from the University of Surrey, UNIX Tutorial for Beginners, is available at:
For PDF files of the handouts see:
All UNIX commands should have a manual (man) page on the machine that you are using e.g. man awk. However sometimes the pages are not installed or are in an unexpected location. It may be more convenient to use a search engine like Google to find information on a command.

6. The basic form of a typical C-shell script
The first line of a C-shell script (text file) is:
#!/bin/csh –f
The –f option tells the script not to source (read) the user’s .cshrc file; this is faster and also makes the script more portable.
All other lines starting with # are comments
Commands may be continued onto subsequent lines with \
Multiple commands can be placed on a single line with ;
Spaces around operators and commands are required but there are no other restrictions

7. The basic form of a typical C-shell script (2)
For neatness, end the script with exit (not essential)
Shell variables start with a $ (this is only omitted with using set - see below)
The shell variable $#argv contains the number of arguments (items) typed on the command line. The items are referred to as shell variables $1, $2, $3, …, $#argv

8. The basic form of a typical C-shell script (3)
For example:
myscript jja yes
would give:
$#argv = 3
$1 = jja
$2 = -4.56
$3= yes

9. The basic form of a typical C-shell script (4)
Shell variables are either string (text) or numeric
A string variable is set (defined) by:
set var = value
e.g. set x = Fred
Note: Variables and values are case-sensitive i.e. x is not the same as X
Variable names can be several characters e.g. set Case2 = 3
To print (display) the value of a variable:
echo $var
e.g. echo $x
Fred

10. The basic form of a typical C-shell script (5)
A numeric variable is set (defined) by:
@ var = integer
k = -7
Simple calculations may be performed
j = ($k + 1) [j would be – = -6]
@ k = ($k + 1) would change k from -7 to -6
Could also use C k ++
@ j = (2 * $k - 5) [k= -7 would give j= -19]
Note: Put spaces around operators like *, + etc.
Floating point operations are not normally used in scripts but can be done with the command bc
e.g. echo " " | bc
would print 8.4 on the screen
set y = `echo " " | bc`
would save the answer in variable y

11. The basic form of a typical C-shell script (6)
A shell variable may be given the output of a command (or user program) as in the bc example. In general:
set var = `command`
e.g. set ff = `ls *.dat`
Remember: ls is used to list files.
If the files are 5.dat 12.dat 13.dat then
echo $ff would display:
5.dat 12.dat 13.dat

12. The basic form of a typical C-shell script (7)
To extract the individual elements of variable ff we can use $#ff to find the number of items (similar to $#argv)
e.g. echo $#ff would display 3
echo $ff[1] would display 5.dat
echo $ff[2] would display 12.dat
echo $ff[3] would display 13.dat

13. The basic form of a typical C-shell script (8)
A while loop is used to set up an iterative or repetitive procedure:
while (condition is true)
commands
end
k = 1 # Initialise k
while ($k <= 3) # Process loop while k <= 3
echo $k # Display k
@ k = ($k + 1) # Increment k by 1

14. The basic form of a typical C-shell script (9)
An if-else-endif structure is used to control script branching:
if (condition 1 is true)
commands
else if (condition 2 is true)
else
endif
Note: use ‘else if` not elseif

15. The basic form of a typical C-shell script (10)
e.g.
if ($x == 6 || $s = sea) then
do something
else if ($x > 10) then
do something else
else
go here if neither of the above conditions is true
endif
Simpler or more complex forms are possible
e.g. if ($y == 2) ls –l *.dat

16. The basic form of a typical C-shell script (11)
The while or if (condition) uses C notation for logical operations:
|| or
&& and
== equal
>= greater than or equal
<= less than or equal
!= not equal
> greater than
< less than

17. The basic form of a typical C-shell script (12)
An example
#!/bin/csh –f
if ($#argv != 1) then
echo “Usage: myscript name”
exit # If incorrect usage end the script
else # If only 1 argument, branch here
set n = ($1) # Put n equal to $1
endif
echo “Your name is “$n
# You could do other things here
exit

18. The basic form of a typical C-shell script (13)
Another example
#!/bin/csh –f
set ff = `ls *.dat` # ff contains filenames *.dat
@ nf = $#ff # nf equals the no. of files (items in ff)
@ j = 1 # Set counter j to 1
while ($j <= $nf) # Loop while j <= nf
set f = $ff[$j] # Set f to be the jth file
ls –l $f # List the details of f
# We could use the file f as an argument to a command or program
myprog $f
@j = ($j + 1) # Increment counter j by 1
end # Go here when j > nf
echo “We are finished!” # A message to the screen
exit

19. Introduction to C-shell programming
Refer to the PDF guide:

20. Advanced UNIX materials
The following are PDF documents that may be used for reference but won’t be discussed in detail during this short course:
Part 1 : Scripts
Part 2 : A summary of useful software
Part 3 : Reanalysis products

21. Lab session Lab session (informal) 2-3:30 PM UNIX Lab
See: